1
|
Peng X, Liu Y, Peng F, Wang T, Cheng Z, Chen Q, Li M, Xu L, Man Y, Zhang Z, Tan Y, Liu Z. Aptamer-controlled stimuli-responsive drug release. Int J Biol Macromol 2024; 279:135353. [PMID: 39245104 DOI: 10.1016/j.ijbiomac.2024.135353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024]
Abstract
Aptamers have been widely researched and applied in nanomedicine due to their programmable, activatable, and switchable properties. However, there are few reviews on aptamer-controlled stimuli-responsive drug delivery. This article highlights the mechanisms and advantages of aptamers in the construction of stimuli-responsive drug delivery systems. We summarize the assembly/reconfiguration mechanisms of aptamers in controlled release systems. The assembly and drug release strategies of drug delivery systems are illustrated. Specifically, we focus on the binding mechanisms to the target and the factors that induce/inhibit the binding to the stimuli, such as strand, pH, light, and temperature. The applications of aptamer-based stimuli-responsive drug release are elaborated. The challenges are discussed, and the future directions are proposed.
Collapse
Affiliation(s)
- Xingxing Peng
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Feicheng Peng
- Hunan Institute for Drug Control, Changsha 410001, Hunan Province, PR China
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Zhongyu Cheng
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Qiwen Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Mingfeng Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Lishang Xu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yunqi Man
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Zhirou Zhang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yifu Tan
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China; Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, PR China.
| |
Collapse
|
2
|
Liu Y, Zhao Z, Zeng Y, He M, Lyu Y, Yuan Q. Thermodynamics and Kinetics-Directed Regulation of Nucleic Acid-Based Molecular Recognition. SMALL METHODS 2024:e2401102. [PMID: 39392199 DOI: 10.1002/smtd.202401102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/28/2024] [Indexed: 10/12/2024]
Abstract
Nucleic acid-based molecular recognition plays crucial roles in various fields like biosensing and disease diagnostics. To achieve optimal detection and analysis, it is essential to regulate the response performance of nucleic acid probes or switches to match specific application requirements by regulating thermodynamics and kinetics properties. However, the impacts of thermodynamics and kinetics theories on recognition performance are sometimes obscure and the relative conclusions are not intuitive. To promote the thorough understanding and rational utilization of thermodynamics and kinetics theories, this review focuses on the landmarks and recent advances of nucleic acid thermodynamics and kinetics and summarizes the nucleic acid thermodynamics and kinetics-based strategies for regulation of nucleic acid-based molecular recognition. This work hopes such a review can provide reference and guidance for the development and optimization of nucleic acid probes and switches in the future, as well as for advancements in other nucleic acid-related fields.
Collapse
Affiliation(s)
- Yihao Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Zihan Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Minze He
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
- Furong Laboratory, Changsha, 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
- Institute of Chemical Biology and Nanomedicine, College of Biology, Hunan University, Changsha, 410082, China
| |
Collapse
|
3
|
Smith FG, Goertz JP, Jurinović K, Stevens MM, Ouldridge TE. Strong sequence-dependence in RNA/DNA hybrid strand displacement kinetics. NANOSCALE 2024; 16:17624-17637. [PMID: 39235130 DOI: 10.1039/d4nr00542b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Strand displacement reactions underlie dynamic nucleic acid nanotechnology. The kinetic and thermodynamic features of DNA-based displacement reactions are well understood and well predicted by current computational models. By contrast, understanding of RNA/DNA hybrid strand displacement kinetics is limited, restricting the design of increasingly complex RNA/DNA hybrid reaction networks with more tightly regulated dynamics. Given the importance of RNA as a diagnostic biomarker, and its critical role in intracellular processes, this shortfall is particularly limiting for the development of strand displacement-based therapeutics and diagnostics. Herein, we characterise 22 RNA/DNA hybrid strand displacement systems, alongside 11 DNA/DNA systems, varying a range of common design parameters including toehold length and branch migration domain length. We observe that differences in stability between RNA-DNA hybrids and DNA-DNA duplexes have large effects on strand displacement rates, with rates for equivalent sequences differing by up to 3 orders of magnitude. Crucially, however, this effect is strongly sequence-dependent, with RNA invaders strongly favoured in a system with RNA strands of high purine content, and disfavoured in a system when the RNA strands have low purine content. These results lay the groundwork for more general design principles, allowing for creation of de novo reaction networks with novel complexity while maintaining predictable reaction kinetics.
Collapse
Affiliation(s)
- Francesca G Smith
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - John P Goertz
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
| | - Križan Jurinović
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Molly M Stevens
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Thomas E Ouldridge
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
4
|
Lee RC, Corsano A, Tseng CY, Laohakunakorn N, Chou LYT. Rewireable Building Blocks for Enzyme-Powered DNA Computing Networks. J Am Chem Soc 2024; 146:26148-26160. [PMID: 39255470 DOI: 10.1021/jacs.4c07221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Neural networks enable the processing of large, complex data sets with applications in disease diagnosis, cell profiling, and drug discovery. Beyond electronic computers, neural networks have been implemented using programmable biomolecules such as DNA; this confers unique advantages, such as greater portability, electricity-free operation, and direct analysis of patterns of biomolecules in solution. Analogous to bottlenecks in electronic computers, the computing power of DNA-based neural networks is limited by the ability to add more computing units, i.e., neurons. This limitation exists because current architectures require many nucleic acids to model a single neuron. Each additional neuron compounds existing problems such as long assembly times, high background signal, and cross-talk between components. Here, we test three strategies to solve this limitation and improve the scalability of DNA-based neural networks: (i) enzymatic synthesis for high-purity neurons, (ii) spatial patterning of neuron clusters based on their network position, and (iii) encoding neuron connectivity on a universal single-stranded DNA backbone. We show that neurons implemented via these strategies activate quickly, with a high signal-to-background ratio and process-weighted inputs. We rewired our modular neurons to demonstrate basic neural network motifs such as cascading, fan-in, and fan-out circuits. Finally, we designed a prototype two-layer microfluidic device to automate the operation of our circuits. We envision that our proposed design will help scale DNA-based neural networks due to its modularity, simplicity of synthesis, and compatibility with various neural network architectures. This will enable portable computing power for applications in portable diagnostics, compact data storage, and autonomous decision making for lab-on-a-chips.
Collapse
Affiliation(s)
- Ryan C Lee
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
| | - Ariel Corsano
- Department of Bioengineering, McGill University, 3480 University Street Room, 350 McConnell Engineering Building, Montreal, Quebec H3A 0E9, Canada
| | - Chung Yi Tseng
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
| | - Nadanai Laohakunakorn
- School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, The King's Buildings, Edinburgh, Scotland EH9 3FF, U.K
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
| |
Collapse
|
5
|
Wang F, Shi B, Chen Y, Shi X, Kou Z, Qiang X. Scalable DNA recognition circuits based on DNA strand displacement. NANOSCALE ADVANCES 2024; 6:4852-4857. [PMID: 39323422 PMCID: PMC11421530 DOI: 10.1039/d4na00379a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/15/2024] [Indexed: 09/27/2024]
Abstract
DNA is a kind of nano-molecule considered to be computable on the molecular level, and the precise Watson-Crick principle of base pairing has made it possible for DNA to be a novel computer material. The DNA strand displacement technology has greatly facilitated the development of DNA computing in both logical and intelligent computation. In this paper, we proposed and implemented a molecular recognition circuit based on DNA strand displacement, which can achieve recognition and summation functions. This circuit has a simple molecular composition and is easily scalable. A cross-inhibition module was integrated based upon the molecular recognition circuit to construct a molecular comparator. Considering the advantages of modularity and the experimental feasibility of a scalable recognition circuit, it could be used as a pattern signal recognition and classification module in smart molecular circuits or biosensors.
Collapse
Affiliation(s)
- Fang Wang
- School of Computer Science and Cyber Engineering, GuangZhou University Guangzhou 510006 China
| | - Beiyu Shi
- Institute of Computing Science and Technology, Guangzhou University Guangzhou 510006 China
| | - Ying Chen
- Institute of Computing Science and Technology, Guangzhou University Guangzhou 510006 China
| | - Xiaolong Shi
- Institute of Computing Science and Technology, Guangzhou University Guangzhou 510006 China
| | - Zheng Kou
- Institute of Computing Science and Technology, Guangzhou University Guangzhou 510006 China
| | - Xiaoli Qiang
- School of Computer Science and Cyber Engineering, GuangZhou University Guangzhou 510006 China
| |
Collapse
|
6
|
Fu S, Li J, Chen J, Zhang L, Liu J, Liu H, Su X. Bacteriophage λ exonuclease and a 5'-phosphorylated DNA guide allow PAM-independent targeting of double-stranded nucleic acids. Nat Biotechnol 2024:10.1038/s41587-024-02388-9. [PMID: 39294394 DOI: 10.1038/s41587-024-02388-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 08/19/2024] [Indexed: 09/20/2024]
Abstract
Sequence-specific recognition of double-stranded nucleic acids is essential for molecular diagnostics and in situ imaging. Clustered regularly interspaced short palindromic repeats and Cas systems rely on protospacer-adjacent motif (PAM)-dependent double-stranded DNA (dsDNA) recognition, limiting the range of targetable sequences and leading to undesired off-target effects. Using single-molecule fluorescence resonance energy transfer analysis, we discover the enzymatic activity of bacteriophage λ exonuclease (λExo). We show binding of 5'-phosphorylated single-stranded DNA (pDNA) to complementary regions on dsDNA and DNA-RNA duplexes, without the need for a PAM-like motif. Upon binding, the λExo-pDNA system catalytically digests the pDNA into nucleotides in the presence of Mg2+. This process is sensitive to mismatches within a wide range of the pDNA-binding region, resulting in exceptional sequence specificity and reduced off-target effects in various applications. The absence of a requirement for a specific motif such as a PAM sequence greatly broadens the range of targets. We demonstrate that the λExo-pDNA system is a versatile tool for molecular diagnostics, DNA computing and gene imaging applications.
Collapse
Affiliation(s)
- Shengnan Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Linghao Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huiyu Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| |
Collapse
|
7
|
Huang C, Shao J, Peng B, Guo Q, Li P, Sun J, Wang Y. Breast Tumor Diagnosis Based on Molecular Learning Vector Quantization Neural Networks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2409150. [PMID: 39290197 DOI: 10.1002/advs.202409150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/11/2024] [Indexed: 09/19/2024]
Abstract
DNA nanotechnology plays a crucial role in precise cancer medicine. Currently, molecular logic circuits are applied to detect tumor-specific biomarkers and control the release of therapeutic drugs. However, these systems lack self-learning capabilities for intelligent diagnostics in biological samples, and their data processing capabilities are limited. Here, a molecular learning vector quantization neural network (LVQNN) model based on DNA strand displacement (DSD) technology for breast tumor diagnosis is developed. Compared to previous work, the molecular LVQNN boasts powerful computing abilities, handling high-dimensional data for intelligent cancer diagnosis. To verify the feasibility and versatility of the network, two distinct typical datasets are selected: one from a single source with cell morphology data from 569 cases, and a more extensive one spanning different populations and ages, with miRNA gene expression data from 1881 cases. By using the molecular LVQNN, diagnostic experiments are conducted on 50 and 120 public individuals from these two datasets, respectively, achieving accuracy rates of 94% and 97.5%. This study demonstrates that the LVQNN model exhibits significant advantages in breast cancer diagnosis and enhances diagnostic accuracy while introducing new approaches for intelligent cancer diagnosis, anticipated to bring significant breakthroughs and application prospects to precise cancer medicine.
Collapse
Affiliation(s)
- Chun Huang
- The School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, China
| | - Jiaying Shao
- The School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, China
| | - Baolei Peng
- The School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, China
| | - Qingshuang Guo
- The School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, China
| | - Panlong Li
- The School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, China
| | - Junwei Sun
- The School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, China
| | - Yanfeng Wang
- The School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, China
| |
Collapse
|
8
|
Guo Z, Deng Y, Yang B, Lu W, Tian Z. Learning from Classic: DNA-Based Conditional Equilibrium Constant To Regulate Affinity "On-the-Fly" for Bioassays. Anal Chem 2024. [PMID: 39276337 DOI: 10.1021/acs.analchem.4c03409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
Artificial programming of affinity is beneficial to optimize responsiveness in biomolecules for various applications. In one classical theory, one comprehensive parameter, conditional equilibrium constant (K'EDTA), can accurately and quantitatively define the affinity of ethylene diamine tetraacetic acid (EDTA) for metal ions. Learning from the classic, we have proposed a novel DNA-based conditional equilibrium constant (K'DNA) to regulate DNA probes' affinity and response "on-the-fly", long after the probe design and synthesis. Artificial regulation of affinity over several magnitudes has been simply realized via short oligonucleotides with different lengths, concentrations, and combinations. The thermodynamic response can be quantitatively simulated by one DNA-based conditional equilibrium constant (K'DNA), acting as an analogue to the classical EDTA system. The proof of concept of affinity programming also allows improved discrimination of single-nucleotide variants as well as assaying ribonuclease and doxycycline in a homogeneous solution. Therefore, the theory of DNA-based conditional equilibrium constant (K'DNA) will enable to engineer versatile DNA switches with programmable affinity in assays and bionanotechnology.
Collapse
Affiliation(s)
- Zihua Guo
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Yinping Deng
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Weiyi Lu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Zhen Tian
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| |
Collapse
|
9
|
Long D, Shi P, Xu X, Ren J, Chen Y, Guo S, Wang X, Cao X, Yang L, Tian Z. Understanding the relationship between sequences and kinetics of DNA strand displacements. Nucleic Acids Res 2024; 52:9407-9416. [PMID: 39077949 PMCID: PMC11381357 DOI: 10.1093/nar/gkae652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 06/18/2024] [Accepted: 07/14/2024] [Indexed: 07/31/2024] Open
Abstract
Precisely modulating the kinetics of toehold-mediated DNA strand displacements (TMSD) is essential for its application in DNA nanotechnology. The sequence in the toehold region significantly influences the kinetics of TMSD. However, due to the large sample space resulting from various arrangements of base sequences and the resulted complex secondary structures, such a correlation is not intuitive. Herein, machine learning was employed to reveal the relationship between the kinetics of TMSD and the toehold sequence as well as the correlated secondary structure of invader strands. Key factors that influence the rate constant of TMSD were identified, such as the number of free hydrogen bonding sites in the invader, the number of free bases in the toehold, and the number of hydrogen bonds in intermediates. Moreover, a predictive model was constructed, which successfully achieved semi-quantitative prediction of rate constants of TMSD even with subtle distinctions in toehold sequence.
Collapse
Affiliation(s)
- Da Long
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Peichen Shi
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Xin Xu
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Jiayi Ren
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Yuqing Chen
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Shihui Guo
- School of Informatics, Xiamen University, Xiamen 361005, PR China
| | - Xinchang Wang
- School of Electronic Science and Engineering (National Model Microelectronics College), Xiamen University, Xiamen 361005, PR China
| | - Xiaoyu Cao
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Zhongqun Tian
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| |
Collapse
|
10
|
Shi R, Chen KL, Fern J, Deng S, Liu Y, Scalise D, Huang Q, Cowan NJ, Gracias DH, Schulman R. Programming gel automata shapes using DNA instructions. Nat Commun 2024; 15:7773. [PMID: 39237499 PMCID: PMC11377784 DOI: 10.1038/s41467-024-51198-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/31/2024] [Indexed: 09/07/2024] Open
Abstract
The ability to transform matter between numerous physical states or shapes without wires or external devices is a major challenge for robotics and materials design. Organisms can transform their shapes using biomolecules carrying specific information and localize at sites where transitions occur. Here, we introduce gel automata, which likewise can transform between a large number of prescribed shapes in response to a combinatorial library of biomolecular instructions. Gel automata are centimeter-scale materials consisting of multiple micro-segments. A library of DNA activator sequences can each reversibly grow or shrink different micro-segments by polymerizing or depolymerizing within them. We develop DNA activator designs that maximize the extent of growth and shrinking, and a photolithography process for precisely fabricating gel automata with elaborate segmentation patterns. Guided by simulations of shape change and neural networks that evaluate gel automata designs, we create gel automata that reversibly transform between multiple, wholly distinct shapes: four different letters and every even or every odd numeral. The sequential and repeated metamorphosis of gel automata demonstrates how soft materials and robots can be digitally programmed and reprogrammed with information-bearing chemical signals.
Collapse
Affiliation(s)
- Ruohong Shi
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuan-Lin Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua Fern
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Siming Deng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Laboratory for Computational Sensing and Robotics (LCSR), Johns Hopkins University, Baltimore, MD, USA
| | - Yixin Liu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Qi Huang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Noah J Cowan
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Laboratory for Computational Sensing and Robotics (LCSR), Johns Hopkins University, Baltimore, MD, USA
| | - David H Gracias
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Center for MicroPhysiological Systems (MPS), Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Laboratory for Computational Sensing and Robotics (LCSR), Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
11
|
Mo F, Li C, Sun J, Lin X, Yu S, Wang F, Liu X, Li J. Programming Fast DNA Amplifier Circuits with Versatile Toehold Exchange Pathway. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2402914. [PMID: 39225421 DOI: 10.1002/smll.202402914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 08/14/2024] [Indexed: 09/04/2024]
Abstract
DNA amplifier circuits establish powerful tools to dynamically control molecular assembly for computation, sensing, and biological applications. However, the slow reaction speed remains a major barrier to their practical utility. Here, diverse fast DNA amplifier circuits termed toehold exchange polymerization (TEP) and toehold exchange catalysis (TEC) using toehold exchange-mediated assembly as a fundamental mechanism are built. Both TEP and TEC with a duplex and a hairpin can respond within minutes to diverse nucleic acid inputs with high fidelity. In addition, the circuits can amplify live-cell signals for fluorescence imaging target RNA dynamics and discriminating different cell lines. Compared with existing DNA circuits that involve time scales of hours for transducing small signals, TEP and TEC exhibit much faster dynamics, simpler design, and comparable sensitivity. These features make TEP and TEC promising platforms to develop programmable nucleic acid tools and devices and to create fast sensing and processing systems, amenable to wide practical applications.
Collapse
Affiliation(s)
- Fengye Mo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Chenbiao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Junlin Sun
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
- Department of Chemistry, Center for Bioanalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Xue Lin
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Shuyi Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
- Beijing Life Science Academy, Beijing, 102209, China
| | - Jinghong Li
- Department of Chemistry, Center for Bioanalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Beijing Life Science Academy, Beijing, 102209, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Center for Bioanalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| |
Collapse
|
12
|
Hasanzadeh A, Ebadati A, Saeedi S, Kamali B, Noori H, Jamei B, Hamblin MR, Liu Y, Karimi M. Nucleic acid-responsive smart systems for controlled cargo delivery. Biotechnol Adv 2024; 74:108393. [PMID: 38825215 DOI: 10.1016/j.biotechadv.2024.108393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.
Collapse
Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arefeh Ebadati
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kamali
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Jamei
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
| |
Collapse
|
13
|
Liu R, Liu T, Liu W, Luo B, Li Y, Fan X, Zhang X, Cui W, Teng Y. SemiSynBio: A new era for neuromorphic computing. Synth Syst Biotechnol 2024; 9:594-599. [PMID: 38711551 PMCID: PMC11070324 DOI: 10.1016/j.synbio.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Neuromorphic computing has the potential to achieve the requirements of the next-generation artificial intelligence (AI) systems, due to its advantages of adaptive learning and parallel computing. Meanwhile, biocomputing has seen ongoing development with the rise of synthetic biology, becoming the driving force for new generation semiconductor synthetic biology (SemiSynBio) technologies. DNA-based biomolecules could potentially perform the functions of Boolean operators as logic gates and be used to construct artificial neural networks (ANNs), providing the possibility of executing neuromorphic computing at the molecular level. Herein, we briefly outline the principles of neuromorphic computing, describe the advances in DNA computing with a focus on synthetic neuromorphic computing, and summarize the major challenges and prospects for synthetic neuromorphic computing. We believe that constructing such synthetic neuromorphic circuits will be an important step toward realizing neuromorphic computing, which would be of widespread use in biocomputing, DNA storage, information security, and national defense.
Collapse
Affiliation(s)
- Ruicun Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Tuoyu Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Wuge Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Boyu Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Yuchen Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Xinyue Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Xianchao Zhang
- Institute of Information Network and Artificial Intelligence, Jiaxing University, Jiaxing, 314001, China
| | - Wei Cui
- South China University of Technology, Guangzhou, 510641, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| |
Collapse
|
14
|
Walbrun A, Wang T, Matthies M, Šulc P, Simmel FC, Rief M. Single-molecule force spectroscopy of toehold-mediated strand displacement. Nat Commun 2024; 15:7564. [PMID: 39217165 PMCID: PMC11365964 DOI: 10.1038/s41467-024-51813-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Toehold-mediated strand displacement (TMSD) is extensively utilized in dynamic DNA nanotechnology and for a wide range of DNA or RNA-based reaction circuits. Investigation of TMSD kinetics typically relies on bulk fluorescence measurements providing effective, bulk-averaged reaction rates. Information on individual molecules or even base pairs is scarce. In this work, we explore the dynamics of strand displacement processes at the single-molecule level using single-molecule force spectroscopy with a microfluidics-enhanced optical trap supported by state-of-the-art coarse-grained simulations. By applying force, we can trigger and observe TMSD in real-time with microsecond and nanometer resolution. We find TMSD proceeds very rapidly under load with single step times of 1 µs. Tuning invasion efficiency by introducing mismatches allows studying thousands of forward/backward invasion events on a single molecule and analyze the kinetics of the invasion process. Extrapolation to zero force reveals single step times for DNA invading DNA four times faster than for RNA invading RNA. We also study the kinetics of DNA invading RNA, a process that in the absence of force would rarely occur. Our results reveal the importance of sequence effects for the TMSD process and have relevance for a wide range of applications in nucleic acid nanotechnology and synthetic biology.
Collapse
Affiliation(s)
- Andreas Walbrun
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Tianhe Wang
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Michael Matthies
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Petr Šulc
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Friedrich C Simmel
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany.
| | - Matthias Rief
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany.
| |
Collapse
|
15
|
Maruyama T, Gong J, Takinoue M. Temporally controlled multistep division of DNA droplets for dynamic artificial cells. Nat Commun 2024; 15:7397. [PMID: 39191726 DOI: 10.1038/s41467-024-51299-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
Synthetic droplets mimicking bio-soft matter droplets formed via liquid-liquid phase separation (LLPS) in living cells have recently been employed in nanobiotechnology for artificial cells, molecular robotics, molecular computing, etc. Temporally controlling the dynamics of synthetic droplets is essential for developing such bio-inspired systems because living systems maintain their functions based on the temporally controlled dynamics of biomolecular reactions and assemblies. This paper reports the temporal control of DNA-based LLPS droplets (DNA droplets). We demonstrate the timing-controlled division of DNA droplets via time-delayed division triggers regulated by chemical reactions. Controlling the release order of multiple division triggers results in order control of the multistep droplet division, i.e., pathway-controlled division in a reaction landscape. Finally, we apply the timing-controlled division into a molecular computing element to compare microRNA concentrations. We believe that temporal control of DNA droplets will promote the design of dynamic artificial cells/molecular robots and sophisticated biomedical applications.
Collapse
Affiliation(s)
- Tomoya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Masahiro Takinoue
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
| |
Collapse
|
16
|
Zhang X, Du R, Xu S, Wang X, Wang ZG. Enhancing DNA-based nanodevices activation through cationic peptide acceleration of strand displacement. NANOSCALE HORIZONS 2024; 9:1582-1586. [PMID: 39036841 DOI: 10.1039/d4nh00252k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Dynamic DNA-based nanodevices offer versatile molecular-level operations, but the majority of them suffer from sluggish kinetics, impeding the advancement of device complexity. In this work, we present the self-assembly of a cationic peptide with DNA to expedite toehold-mediated DNA strand displacement (TMSD) reactions, a fundamental mechanism enabling the dynamic control and actuation of DNA nanostructures. The target DNA is modified with a fluorophore and a quencher, so that the TMSD process can be monitored by recording the time-dependent fluorescence changes. The boosting effect of the peptides is found to be dependent on the peptide/DNA N/P ratio, the toehold/invader binding affinity, and the ionic strength with stronger effects observed at lower ionic strengths, suggesting that electrostatic interactions play a key role. Furthermore, we demonstrate that the cationic peptide enhances the responsiveness and robustness of DNA machinery tweezers or logic circuits (AND and OR) involving multiple strand displacement reactions in parallel and cascade, highlighting its broad utility across DNA-based systems of varying complexity. This work offers a versatile approach to enhance the efficiency of toehold-mediated DNA nanodevices, facilitating flexible design and broader applications.
Collapse
Affiliation(s)
- Xianxue Zhang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Ruikai Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xinyue Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
17
|
Makino K, Sugiyama I, Asanuma H, Kashida H. Kinetics of Strand Displacement Reaction with Acyclic Artificial Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202319864. [PMID: 38840525 DOI: 10.1002/anie.202319864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Toehold-mediated strand displacement (TMSD) reaction, one of the DNA nanotechnologies, has great potential as s biological programmable platform in the cellular environment. Various artificial nucleic acids have been developed to improve stability and affinity for biological applications. However, the lack of understanding of the kinetics of TMSD reaction among artificial nucleic acids has limited their applications. We herein systematically characterized the kinetics of TMSD reactions with acyclic xeno nucleic acids (XNAs): serinol nucleic acid (SNA), acyclic D-threoninol nucleic acid (D-aTNA), and acyclic L-threoninol nucleic acid (L-aTNA). We found that the strand displacement reactions by D-aTNA and by L-aTNA were highly dependent on temperature. D-aTNA and L-aTNA systems were orthogonal to each other, and chirality of the input can be switched by using SNA as an interface. We also applied TMSD reactions of XNAs to a seesaw gate amplification system which utilizes the orthogonality. This work will contribute to the developments of thermoresponsive and bioorthogonal nucleic acid circuits.
Collapse
Affiliation(s)
- Koki Makino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Itsumi Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| |
Collapse
|
18
|
Lin N, Ouyang Y, Qin Y, Karmi O, Sohn YS, Liu S, Nechushtai R, Zhang Y, Willner I, Zhou Z. Spatially Localized Entropy-Driven Evolution of Nucleic Acid-Based Constitutional Dynamic Networks for Intracellular Imaging and Spatiotemporal Programmable Gene Therapy. J Am Chem Soc 2024; 146:20685-20699. [PMID: 39012486 PMCID: PMC11295181 DOI: 10.1021/jacs.4c03651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024]
Abstract
The primer-guided entropy-driven high-throughput evolution of the DNA-based constitutional dynamic network, CDN, is introduced. The entropy gain associated with the process provides a catalytic principle for the amplified emergence of the CDN. The concept is applied to develop a programmable, spatially localized DNA circuit for effective in vitro and in vivo theranostic, gene-regulated treatment of cancer cells. The localized circuit consists of a DNA tetrahedron core modified at its corners with four tethers that include encoded base sequences exhibiting the capacity to emerge and assemble into a [2 × 2] CDN. Two of the tethers are caged by a pair of siRNA subunits, blocking the circuit into a mute, dynamically inactive configuration. In the presence of miRNA-21 as primer, the siRNA subunits are displaced, resulting in amplified release of the siRNAs silencing the HIF-1α mRNA and fast dynamic reconfiguration of the tethers into a CDN. The resulting CDN is, however, engineered to be dynamically reconfigured by miRNA-155 into an equilibrated mixture enriched with a DNAzyme component, catalyzing the cleavage of EGR-1 mRNA. The DNA tetrahedron nanostructure stimulates enhanced permeation into cancer cells. The miRNA-triggered entropy-driven reconfiguration of the spatially localized circuit leads to the programmable, cooperative bis-gene-silencing of HIF-1α and EGR-1 mRNAs, resulting in the effective and selective apoptosis of breast cancer cells and effective inhibition of tumors in tumor bearing mice.
Collapse
Affiliation(s)
- Nina Lin
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| | - Yu Ouyang
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yunlong Qin
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ola Karmi
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Songqin Liu
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| | - Rachel Nechushtai
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Yuanjian Zhang
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhixin Zhou
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| |
Collapse
|
19
|
Schaffter SW, Kengmana E, Fern J, Byrne SR, Schulman R. Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes. ACS Synth Biol 2024; 13:1964-1977. [PMID: 38885464 DOI: 10.1021/acssynbio.3c00726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Bacteriophage RNA polymerases, in particular T7 RNA polymerase (RNAP), are well-characterized and popular enzymes for many RNA applications in biotechnology both in vitro and in cellular settings. These monomeric polymerases are relatively inexpensive and have high transcription rates and processivity to quickly produce large quantities of RNA. T7 RNAP also has high promoter-specificity on double-stranded DNA (dsDNA) such that it only initiates transcription downstream of its 17-base promoter site on dsDNA templates. However, there are many promoter-independent T7 RNAP transcription reactions involving transcription initiation in regions of single-stranded DNA (ssDNA) that have been reported and characterized. These promoter-independent transcription reactions are important to consider when using T7 RNAP transcriptional systems for DNA nanotechnology and DNA computing applications, in which ssDNA domains often stabilize, organize, and functionalize DNA nanostructures and facilitate strand displacement reactions. Here we review the existing literature on promoter-independent transcription by bacteriophage RNA polymerases with a specific focus on T7 RNAP, and provide examples of how promoter-independent reactions can disrupt the functionality of DNA strand displacement circuit components and alter the stability and functionality of DNA-based materials. We then highlight design strategies for DNA nanotechnology applications that can mitigate the effects of promoter-independent T7 RNAP transcription. The design strategies we present should have an immediate impact by increasing the rate of success of using T7 RNAP for applications in DNA nanotechnology and DNA computing.
Collapse
Affiliation(s)
- Samuel W Schaffter
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eli Kengmana
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joshua Fern
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Shane R Byrne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
20
|
Mukherjee R, Sengar A, Cabello-García J, Ouldridge TE. Kinetic Proofreading Can Enhance Specificity in a Nonenzymatic DNA Strand Displacement Network. J Am Chem Soc 2024; 146:18916-18926. [PMID: 38951503 PMCID: PMC11258683 DOI: 10.1021/jacs.3c14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024]
Abstract
Kinetic proofreading is used throughout natural systems to enhance the specificity of molecular recognition. At its most basic level, kinetic proofreading uses a supply of chemical fuel to drive a recognition interaction out of equilibrium, allowing a single free-energy difference between correct and incorrect targets to be exploited two or more times. Despite its importance in biology, there has been little effort to incorporate kinetic proofreading into synthetic systems in which molecular recognition is important, such as nucleic acid nanotechnology. In this article, we introduce a DNA strand displacement-based kinetic proofreading motif, showing that the consumption of a DNA-based fuel can be used to enhance molecular recognition during a templated dimerization reaction. We then show that kinetic proofreading can enhance the specificity with which a probe discriminates single nucleotide mutations, both in terms of the initial rate with which the probe reacts and the long-time behavior.
Collapse
Affiliation(s)
- Rakesh Mukherjee
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
| | - Aditya Sengar
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
| | | | | |
Collapse
|
21
|
Hu Y, Cui Y, Zhang Z, Zhang X, Ma X, Qiao Z, Zheng F, Feng F, Liu W, Han L. A Dual-Recognition Fluorescence Enzyme-Linked Immunosorbent Assay for Specific Detection of Intact Lipid Nanoparticles via a Localized Scaffolding Autocatalytic DNA Circuit Amplifier. Anal Chem 2024; 96:11205-11215. [PMID: 38967035 DOI: 10.1021/acs.analchem.4c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Lipid nanoparticles (LNPs) are emerging as one of the most promising drug delivery systems. The long-circulating effect of intact LNPs (i-LNPs) is the key to efficacy and toxicity in vivo. However, the significant challenge is specific and sensitive detection of i-LNPs. Herein, a dual-recognition fluorescence enzyme-linked immunosorbent assay (DR-FELISA) was developed to directly isolate and detect i-LNPs by combining dual-recognition separation with a one-step signal amplification strategy. The microplates captured and enriched i-LNPs through antibody-antigen reaction. Dual-chol probes were spontaneously introduced into the lipid bilayer of captured i-LNPs, converting the detection of i-LNPs into the detection of double-cholesterol probes. Finally, the end of the dual-chol probes initiated the localized scaffolding autocatalytic DNA circuits (SADC) system for further signal amplification. The SADC system provides a sensitive and efficient amplifier through localized network structures and self-assembled triggers. Simultaneous recognition of i-LNPs surface PEG-lipid and lipid bilayer structures significantly eliminates interference from biological samples. i-LNPs were detected with high selectivity, ranging from 0.2 to 1.25 mg/mL with a limit of detection of 0.1 mg/mL. Moreover, this method allows the isolation and quantitative analysis of different formulations of i-LNPs in serum samples with a satisfactory recovery rate ranging from 94.8 to 116.3%. Thus, the DR-FELISA method provides an advanced platform for the exclusive and sensitive detection of i-LNPs, providing new insights for the study of the quality and intracorporal process of complex formulations.
Collapse
Affiliation(s)
- Yexin Hu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Yuqing Cui
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Zhemeng Zhang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Xinyi Zhang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Xiao Ma
- Gansu Institute for Drug Control, Gansu 730000, China
| | - Zhou Qiao
- China Pharmaceutical University Center for Analysis and Testing, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Zheng
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Feng
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
- Zhejiang Center for Safety Study of Drug Substances (Industrial Technology Innovation Platform), Hangzhou 310018, China
| | - Lingfei Han
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
- Zhejiang Center for Safety Study of Drug Substances (Industrial Technology Innovation Platform), Hangzhou 310018, China
| |
Collapse
|
22
|
Zhang Q, Wei Z, Jia X. Controllable detection threshold achieved through the toehold switch system in a mercury ion whole-cell biosensor. Biosens Bioelectron 2024; 256:116283. [PMID: 38608495 DOI: 10.1016/j.bios.2024.116283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Due to the toxicity of mercury and its harmful effects on human health, it is essential to establish a low-cost, highly sensitive and highly specific monitoring method with a wide detection range, ideally with a simple visual readout. In this study, a whole-cell biosensor with adjustable detection limits was developed for the detection of mercury ions in water samples, allowing controllable threshold detection with an expanded detection range. Gene circuits were constructed by combining the toehold switch system with lactose operon, mercury-ion-specific operon, and inducible red fluorescent protein gene. Using MATLAB for design and selection, a total of eleven dual-input single-output sensing logic circuits were obtained based on the basic logic of gene circuit construction. Then, biosensor DTS-3 was selected based on its fluorescence response at different isopropyl β-D-Thiogalactoside (IPTG) concentrations, exhibiting the controllable detection threshold. At 5-20 μM IPTG, DTS-3 can achieve variable threshold detection in the range of 0.005-0.0075, 0.06-0.08, 1-2, and 4-6 μM mercury ion concentrations, respectively. Specificity experiments demonstrated that DTS-3 exhibits good specificity, not showing fluorescence response changes compared with other metal ions. Furthermore spiked sample experiments demonstrated its good resistance to interference, allowing it to distinguish mercury ion concentrations as low as 7.5 nM by the naked eye and 5 nM using a microplate reader. This study confirms the feasibility and performance of biosensor with controllable detection threshold, providing a new detection method and new ideas for expanding the detection range of biosensors while ensuring rapid and convenient measurements without compromising sensitivity.
Collapse
Affiliation(s)
- Qinglong Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.
| | - Zixiang Wei
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, PR China.
| |
Collapse
|
23
|
Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches. Chem 2024; 10:2220-2244. [PMID: 39036067 PMCID: PMC11259118 DOI: 10.1016/j.chempr.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. We describe a class of aptamer-based RNA switches or aptaswitches that recognize target nucleic acid molecules and initiate folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide an intense fluorescent readout without intervening enzymes, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. Aptaswitches can be used to regulate folding of seven fluorogenic aptamers, providing a general means of controlling aptamers and an array of multiplexable reporter colors. Coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed all-in-one reactions against RNA from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that are readily integrated into rapid diagnostic assays.
Collapse
Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Nery R. Arevalos
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Zachary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts
Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT,
Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA,
USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School,
Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
- Lead contact
| |
Collapse
|
24
|
Liu Y, Zhai Y, Hu H, Liao Y, Liu H, Liu X, He J, Wang L, Wang H, Li L, Zhou X, Xiao X. Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400011. [PMID: 38698560 PMCID: PMC11234411 DOI: 10.1002/advs.202400011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/09/2024] [Indexed: 05/05/2024]
Abstract
DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.
Collapse
Affiliation(s)
- Yizhou Liu
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuxuan Zhai
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hao Hu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuheng Liao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Huan Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiao Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Jiachen He
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Limei Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hongxun Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Longjie Li
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000China
| | - Xianjin Xiao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| |
Collapse
|
25
|
Qin Y, Huang F, Tang Q, Li J, Zhang H, Luo K, Zhou J, Wang H, Wang L, Li L, Xiao X. Inhibition of kinetic random-distribution in DNA Seesaw gates and biosensors for complete leakage prevention. Biosens Bioelectron 2024; 255:116203. [PMID: 38531225 DOI: 10.1016/j.bios.2024.116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/17/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
DNA nanomaterials have a wide application prospect in biomedical field, among which DNA computers and biosensors based on Seesaw-based DNA circuit is considered to have the most development potential. However, the serious leakage of Seesaw-based DNA circuit prevented its further development and application. Moreover, the existing methods to suppress leakage can't achieve the ideal effect. Interestingly, we found a new source of leakage in Seesaw-based DNA circuit, which we think is the main reason why the previous methods to suppress leakage are not satisfactory. Therefore, based on this discovery, we use DNA triplex to design a new method to suppress the leakage of Seesaw-based DNA circuit. Its ingenious design makes it possible to perfectly suppress the leakage of all sources in Seesaw-based DNA circuit and ensure the normal output of the circuit. Based on this technology, we have constructed basic Seesaw module, AND gate, OR gate, secondary complex circuits and DNA detector. Experimental results show that we can increase the working range of the secondary Seesaw-based DNA circuit by five folds and keep its normal output signal above 90%, and we can improve the LOD of the Seesaw-based DNA detector to 1/11 of the traditional one(1.8pM). More importantly, we successfully developed a detector with adjustable detection range, which can theoretically achieve accurate detection in any concentration range. We believe the established triplex blocking strategy will greatly facilitate the most powerful Seesaw based DNA computers and biosensors, and further promote its application in biological systems.
Collapse
Affiliation(s)
- Yang Qin
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China; Institute of Reproductive Health, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Pancreatic Surgery, Union Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Feiyang Huang
- Institute of Reproductive Health, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qi Tang
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiangtian Li
- Institute of Reproductive Health, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Heao Zhang
- Institute of Reproductive Health, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kuangdi Luo
- Institute of Reproductive Health, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiahui Zhou
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Hongxun Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Longjie Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China; Institute of Reproductive Health, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College Huazhong University of Science and Technology, Wuhan, 430030, China.
| |
Collapse
|
26
|
Wang Y, Jin P, Kumar A, Jan L, Cheng Y, Jan YN, Zhang Y. Nonlinear compliance of NompC gating spring and its implication in mechanotransduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599842. [PMID: 38979198 PMCID: PMC11230213 DOI: 10.1101/2024.06.20.599842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Cytoskeleton-tethered mechanosensitive channels (MSCs) utilize compliant proteins or protein domains called gating springs to convert mechanical stimuli into electric signals, enabling sound and touch sensation and proprioception. The mechanical properties of these gating springs, however, remain elusive. Here, we explored the mechanical properties of the homotetrameric NompC complex containing long ankyrin-repeat domains (ARDs). We developed a toehold-mediated strand displacement approach to tether single membrane proteins, allowing us to exert force on them and precisely measure their absolute extension using optical tweezers. Our findings revealed that each ARD has a low stiffness of ~0.7 pN/nm and begins to unfold stepwise at ~7 pN, leading to nonlinear compliance. Our calculations indicate that this nonlinear compliance may help regulate NompC's sensitivity, dynamic range, and kinetics to detect mechanical stimuli. Overall, our research highlights the importance of a compliant and unfolding-refolding gating spring in facilitating a graded response of MSC ion transduction across a wide spectrum of mechanical stimuli.
Collapse
Affiliation(s)
- Yukun Wang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Peng Jin
- Department of Physiology, University of California, San Francisco, CA, USA
| | - Avinash Kumar
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Lily Jan
- Department of Physiology, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, UCSF, San Francisco, CA, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, UCSF, San Francisco, CA, USA
| | - Yuh-Nung Jan
- Department of Physiology, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, UCSF, San Francisco, CA, USA
| | - Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| |
Collapse
|
27
|
Na H, Koo BI, Park JC, Lim J, Kim Y, Chung HJ, Nam YS. Live-Cell Imaging of MicroRNA Expression via Photoinduced Electron Transfer Controlled by Catalytic Hairpin Assembly. Adv Healthc Mater 2024:e2401483. [PMID: 38889395 DOI: 10.1002/adhm.202401483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 06/20/2024]
Abstract
MicroRNAs (miRNAs) serve as emerging biomarkers for a range of diseases, and their quantitative analysis draws increasing attention. Yet, current invasive methods limit continuous tracking within living cells. To overcome this, a nonenzymatic DNA-based nanoprobe is developed for dynamic, noninvasive miRNA tracking via live-cell imaging. This probe features a unique hairpin DNA structure with five guanines that act as internal quenchers, suppressing fluorescence from an attached fluorophore via photoinduced electron transfer. Target miRNA initiates toehold-mediated strand displacement, restoring, and amplifying the fluorescence signal. Additionally, by introducing a single mismatch to the hairpin DNA, the nanoprobe's sensitivity is significantly enhanced, lowering the detection limit to about 60 pM without compromising specificity. To optimize intracellular delivery for prolonged monitoring, the nanoprobe is encapsulated within multilamellar lipid nanovesicles, fluorescently labeled for dual-wavelength ratiometric analysis. The proposed nanoprobe demonstrates a significant advance in live-cell miRNA detection, promising enhanced in situ analysis for a better understanding of miRNAs' pathophysiological function.
Collapse
Affiliation(s)
- Hyebin Na
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Bon Il Koo
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jae Chul Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jiwoo Lim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Jung Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yoon Sung Nam
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| |
Collapse
|
28
|
Kawamata I, Nishiyama K, Matsumoto D, Ichiseki S, Keya JJ, Okuyama K, Ichikawa M, Kabir AMR, Sato Y, Inoue D, Murata S, Sada K, Kakugo A, Nomura SIM. Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller. SCIENCE ADVANCES 2024; 10:eadn4490. [PMID: 38820146 PMCID: PMC11141615 DOI: 10.1126/sciadv.adn4490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the programmability of DNA are regarded as promising components for these systems. However, current systems rely on the manual addition of external stimuli, limiting the potential for autonomous molecular systems. Here, we show that DNA-based cascade reactions can act as a molecular controller that drives the autonomous assembly and disassembly of DNA-functionalized microtubules propelled by kinesins. The DNA controller is designed to produce two different DNA strands that program the interaction between the microtubules. The gliding microtubules integrated with the controller autonomously assemble to bundle-like structures and disassemble into discrete filaments without external stimuli, which is observable by fluorescence microscopy. We believe this approach to be a starting point toward more autonomous behavior of motor protein-based multicomponent systems with robotic functionalities.
Collapse
Affiliation(s)
- Ibuki Kawamata
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kohei Nishiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Daiki Matsumoto
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Shosei Ichiseki
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Jakia J. Keya
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kohei Okuyama
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, Iizuka 820-8502, Japan
| | - Daisuke Inoue
- Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | - Satoshi Murata
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | |
Collapse
|
29
|
Tosti Guerra F, Poppleton E, Šulc P, Rovigatti L. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems. J Chem Phys 2024; 160:205102. [PMID: 38814009 DOI: 10.1063/5.0202829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/04/2024] [Indexed: 05/31/2024] Open
Abstract
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model.
Collapse
Affiliation(s)
- F Tosti Guerra
- Department of Physics, Sapienza University of Rome, Roma, Italy
| | - E Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - P Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Department of Bioscience, School of Natural Sciences, Technical University Munich, Munich, Germany
| | - L Rovigatti
- Department of Physics, Sapienza University of Rome, Roma, Italy
| |
Collapse
|
30
|
Wang L, Bu S, Xu S, Huang T, Yang F, Tan Q, Deng M, Xie W, Cai B, Chen J. Double base mismatches mediated catalytic hairpin assembly for enzyme-free single-base mutation detection: integrating signal recognition and amplification in one. Mikrochim Acta 2024; 191:334. [PMID: 38758362 DOI: 10.1007/s00604-024-06366-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/14/2024] [Indexed: 05/18/2024]
Abstract
Single nucleotide polymorphism (SNP) biosensors are emerging rapidly for their promising applications in human disease prevention diagnosis, treatment, and prognosis. However, it remains a bottleneck in equipping simple and stable biosensors with the traits of high sensitivity, non-enzyme, and low cost. Double base mismatches mediated chain displacement reactions have attracted fascinating advantages of tailorable thermodynamics stability, non-enzyme, and excellent assembly compliance to involvement in SNP identification. As the base mismatch position and amount in DNA sequence can be artificially adjusted, it provides plenty of selectivity and specificity for exploring perfect biosensors. Herein, a biosensor with double base mismatches mediated catalytic hairpin assembly (CHA) is designed via one base mismatch in the toehold domain and the other base mismatch in the stem sequence of hairpin 1 (H1) by triggering CHA reaction to achieve selective amplification of the mutation target (MT) and fluorescence resonance energy transfer (FRET) effect that is composed of Cy3 and Cy5 terminally attached H1 and hairpin 2 (H2). Depending on the rationally designed base mismatch position and toehold length, the fabricated biosensors show superior SNP detection performance, exhibiting a good linearity with high sensitivity of 6.6 fM detection limit and a broad detection abundance of 1%. The proposed biosensor can be used to detect the KRAS mutation gene in real samples and obtain good recoveries between 106 and 116.99%. Remarkably, these extendible designs of base mismatches can be used for more types of SNP detection, providing flexible adjustment based on base mismatch position and toehold length variations, especially for their thermodynamic model for DNA-strand displacement reactions.
Collapse
Affiliation(s)
- Lanyue Wang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Sisi Bu
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Shijie Xu
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Tuo Huang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Fang Yang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Qianglong Tan
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Minxin Deng
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Wenlin Xie
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
| | - Bobo Cai
- Zhejiang Hospital, Hangzhou, 310013, China.
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
| |
Collapse
|
31
|
Wang L, Luo W, Weng Z, Wang Z, Wu Y, Zhao R, Han X, Liu X, Zhang J, Yang Y, Xie G. Building a stable and robust anti-interference DNA dissipation system by eliminating the accumulation of systemic specified errors. Anal Chim Acta 2024; 1302:342493. [PMID: 38580407 DOI: 10.1016/j.aca.2024.342493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND The emergence of DNA nanotechnology has enabled the systematic design of diverse bionic dissipative behaviors under the precise control of nucleic acid nanodevices. Nevertheless, when compared to the dissipation observed in robust living systems, it is highly desirable to enhance the anti-interference for artificial DNA dissipation to withstand perturbations and facilitate repairs within the complex biological environments. RESULTS In this study, we introduce strategically designed "trash cans" to facilitate kinetic control over interferences, transforming the stochastic binding of individual components within a homogeneous solution into a competitive binding process. This approach effectively eliminates incorrect binding and the accumulation of systemic interferences while ensuring a consistent pattern of energy fluctuation from response to silence. Remarkably, even in the presence of numerous interferences differing by only one base, we successfully achieve complete system reset through multiple cycles, effectively restoring the energy level to a minimum. SIGNIFICANCE The system was able to operate stably without any adverse effect under conditions of irregular interference, high-abundance interference, and even multiplex interferences including DNA and RNA crosstalk. This work not only provides an effective paradigm for constructing robust DNA dissipation systems but also greatly broadens the potential of DNA dissipation for applications in high-precision molecular recognition and complex biological reaction networks.
Collapse
Affiliation(s)
- Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - You Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xin Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Jianhong Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
| |
Collapse
|
32
|
Wang X, Chen T, Ping Y, Dai Y, Yu P, Xie Y, Liu Z, Sun B, Duan X, Tao Z. Sequence-Guided Localization of DNA Hybridization Enables Highly Selective and Robust Genotyping. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307985. [PMID: 38084466 DOI: 10.1002/smll.202307985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/28/2023] [Indexed: 05/18/2024]
Abstract
Genetic variations are always related to human diseases or susceptibility to therapies. Nucleic acid probes that precisely distinguish closely related sequences become an indispensable requisite both in research and clinical applications. Here, a Sequence-guided DNA LOCalization for leaKless DNA detection (SeqLOCK) is introduced as a technique for DNA hybridization, where the intended targets carrying distinct "guiding sequences" act selectively on the probes. In silicon modeling, experimental results reveal considerable agreement (R2 = 0.9228) that SeqLOCK is capable of preserving high discrimination capacity at an extraordinarily wide range of target concentrations. Furthermore, SeqLOCK reveals high robustness to various solution conditions and can be directly adapted to nucleic acid amplification techniques (e.g., polymerase chain reaction) without the need for laborious pre-treatments. Benefiting from the low hybridization leakage of SeqLOCK, three distinct variations with a clinically relevant mutation frequency under the background of genomic DNA can be discriminated simultaneously. This work establishes a reliable nucleic acid hybridization strategy that offers great potential for constructing robust and programmable systems for molecular sensing and computing.
Collapse
Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Tao Chen
- Department of Blood Transfusion, Zhejiang Hospital, Hangzhou, 310052, China
| | - Ying Ping
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Yibei Dai
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Pan Yu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Yiyi Xie
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Zhenping Liu
- Department of Laboratory Medicine, Yuhang Branch of the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310058, China
| | - Bohao Sun
- Department of Pathology, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009, China
| | - Xiuzhi Duan
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Zhihua Tao
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| |
Collapse
|
33
|
Akay A, Reddy HN, Galloway R, Kozyra J, Jackson AW. Predicting DNA toehold-mediated strand displacement rate constants using a DNA-BERT transformer deep learning model. Heliyon 2024; 10:e28443. [PMID: 38560216 PMCID: PMC10981123 DOI: 10.1016/j.heliyon.2024.e28443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Dynamic DNA nanotechnology is driving exciting developments in molecular computing, cargo delivery, sensing and detection. Combining this innovative area of research with the progress made in machine learning will aid in the design of sophisticated DNA machinery. Herein, we present a novel framework based on a transformer architecture and a deep learning model which can predict the rate constant of toehold-mediated strand displacement, the underlying process in dynamic DNA nanotechnology. Initially, a dataset of 4450 DNA sequences and corresponding rate constants were generated in-silico using KinDA. Subsequently, a 1D convolution neural network was trained using specific local features and DNA-BERT sequence embedding to produce predicted rate constants. As a result, the newly trained deep learning model predicted toehold-mediated strand displacement rate constants with a root mean square error of 0.76, during testing. These findings demonstrate that DNA-BERT can improve prediction accuracy, negating the need for extensive computational simulations or experimentation. Finally, the impact of various local features during model training is discussed, and a detailed comparison between the One-hot encoder and DNA-BERT sequences representation methods is presented.
Collapse
Affiliation(s)
- Ali Akay
- Nanovery Limited, United Kingdom
- Universita Degli Studi di Trento, Italy
| | | | | | | | | |
Collapse
|
34
|
Zhang M, Yancey C, Zhang C, Wang J, Ma Q, Yang L, Schulman R, Han D, Tan W. A DNA circuit that records molecular events. SCIENCE ADVANCES 2024; 10:eadn3329. [PMID: 38578999 PMCID: PMC10997190 DOI: 10.1126/sciadv.adn3329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Characterizing the relative onset time, strength, and duration of molecular signals is critical for understanding the operation of signal transduction and genetic regulatory networks. However, detecting multiple such molecules as they are produced and then quickly consumed is challenging. A MER can encode information about transient molecular events as stable DNA sequences and are amenable to downstream sequencing or other analysis. Here, we report the development of a de novo molecular event recorder that processes information using a strand displacement reaction network and encodes the information using the primer exchange reaction, which can be decoded and quantified by DNA sequencing. The event recorder was able to classify the order at which different molecular signals appeared in time with 88% accuracy, the concentrations with 100% accuracy, and the duration with 75% accuracy. This simultaneous and highly programmable multiparameter recording could enable the large-scale deciphering of molecular events such as within dynamic reaction environments, living cells, or tissues.
Collapse
Affiliation(s)
- Mingzhi Zhang
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Colin Yancey
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chao Zhang
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Intellinosis Biotech Co. Ltd., Shanghai, 201112, China
| | - Junyan Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Qian Ma
- Intellinosis Biotech Co. Ltd., Shanghai, 201112, China
| | - Linlin Yang
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Da Han
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
35
|
Sugawara T, Oishi M. Latent Toehold-Mediated DNA Circuits Based on a Bulge-Loop Structure for Leakage Reduction and Its Application to Signal-Amplifying DNA Logic Gates. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15907-15915. [PMID: 38508218 DOI: 10.1021/acsami.3c19344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
DNA circuits based on successive toehold-mediated DNA displacement reactions, particularly entropy-driven DNA circuit (EDC) systems, have attracted considerable attention as powerful enzyme-free tools for dynamic DNA nanotechnology. However, background leakage (noise signal) often occurs when the circuit is executed nonspecifically, even in the absence of the appropriate catalyst DNA (input). This study designed and developed a new latent toehold-mediated DNA circuit (LDC) system that relies on a bulge-loop structure as a latent toehold toward leakage reduction. Furthermore, the number (size) of nucleotides (nt) in the bulge-loop is found to play a significant role in the performance (i.e., leakage, signal, and kinetics) of LDC systems. In fact, the signal rate for the LDC systems increased as the number of nt in the bulge-loop increased from 4 to 8, whereas the leakage rate of the LDC systems with bulge-loops of 7 nt or less was low, but the leakage rate of the LDC system with a bulge-loop of 8 nt increased significantly. Note that the LDC system with the optimal bulge-loop (7 nt) was capable of not only reducing the leakage but also accelerating the circuit speed without any signal loss, unlike methods of reducing the leakage by reducing the signal reported previously for the conventional EDC systems. These facts indicate that the 7 nt bulge-loop acts as a "latent" toehold for the DNA circuit system. By using the amplification function of output signals with an accelerated circuit and reduced leakage, our LDC system with a 7 nt bulge-loop could be applied directly and successfully to signal-amplifying DNA logic gates such as OR and AND gates, and thus, sufficient output signals could be obtained even with a small amount of input. These findings reveal that our LDC systems with a bulge-loop structure can replace the conventional EDC system and have enormous potential in the field of DNA nanotechnology.
Collapse
Affiliation(s)
- Taku Sugawara
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
| | - Motoi Oishi
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
| |
Collapse
|
36
|
Frommer J, Oppenheimer R, Allott BM, Núñez-Pertíñez S, Wilks TR, Cox LR, Bath J, O'Reilly RK, Turberfield AJ. A New Architecture for DNA-Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation. Angew Chem Int Ed Engl 2024; 63:e202317482. [PMID: 38346169 DOI: 10.1002/anie.202317482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Indexed: 03/01/2024]
Abstract
The synthesis of artificial sequence-defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA-templated reactions. Here, we report an architecture for DNA-templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA-templated reaction. This protective effect has the potential to overcome the challenges associated with programmable, sequence-controlled synthesis of long non-natural polymers by extending the lifetime of the reactive building blocks.
Collapse
Affiliation(s)
- Jennifer Frommer
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Robert Oppenheimer
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - Benjamin M Allott
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Samuel Núñez-Pertíñez
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Thomas R Wilks
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Liam R Cox
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Andrew J Turberfield
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| |
Collapse
|
37
|
Ye J, Huang W, Jia X, Song H, Zhou Y, Yuan R, Xu W. Short-stranded DNA segment-modulated LAMP/H + as signal transducer to guide CHA-cooperated amplifiable electrochemical biosensing. Anal Chim Acta 2024; 1295:342329. [PMID: 38355233 DOI: 10.1016/j.aca.2024.342329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Modulating loop-mediated isothermal amplification (mLAMP) by short-stranded DNA segment trigger (T) to generate byproducts H+ ions (mLAMP/H+) as signal transducer is intriguing for developing catalytic hairpin assembly (CHA)-cooperated amplifiable electrochemical biosensors. This would be a big challenge for traditional LAMP that is basically suitable for amplifying long-stranded oligonucleotides up to 200-300 nt. To address this inherent limitation of traditional LAMP, many researchers have put in efforts to explore improvements in this that would allow LAMP to be used for a wider range of target species amplification. RESULTS Here in this work, we are inspired to explore two-step loop-mediated amplification, firstly forming T-activated double-loop dumbbell structure (DLDS) intermediate by a recognition hairpin and a hairpin precursor, and next DLDS-guided mLAMP process with the aid of two primers to yield mLAMP/H+ during successive DNA incorporation via nucleophilic attacking interaction. To manipulate the mLAMP/H+-directed transduction of input T, a pH-responsive triplex strand is designed with the ability of self-folding in Hoogsteen structure at slightly acidic conditions, resulting in the dehybridization of a fuel strand (FS) to participate in CHA between two hairpins on the modified electrode surface, in which FS is repetitively displaced and recycled to fuel the progressive CHA events. In the as-assembled dsDNA complexes, numerous electroactive ferrocene labels are immobilized in the electrode sensing interface, thereby generating significantly amplified electrochemical current signal that can sense the presented and varied T. SIGNIFICANCE It is clear that we have creatively constructed a unique electrochemical biosensor for disease detection. Benefited from the rational combination of mLAMP and CHA, our electrochemical strategy is highly sensitive, specific and simplified, and would provide a new paradigm to construct various mLAMP/H+-based biosensors for other short-stranded DNA or microRNAs markers.
Collapse
Affiliation(s)
- Jingjing Ye
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Xinyue Jia
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Honglin Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yifu Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| |
Collapse
|
38
|
Todisco M, Ding D, Szostak JW. Transient states during the annealing of mismatched and bulged oligonucleotides. Nucleic Acids Res 2024; 52:2174-2187. [PMID: 38348869 PMCID: PMC10954449 DOI: 10.1093/nar/gkae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12 bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully versus partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.
Collapse
Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
39
|
Ratajczyk EJ, Šulc P, Turberfield AJ, Doye JPK, Louis AA. Coarse-grained modeling of DNA-RNA hybrids. J Chem Phys 2024; 160:115101. [PMID: 38497475 DOI: 10.1063/5.0199558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 03/19/2024] Open
Abstract
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA-RNA hydrogen bonding interaction, we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability, we provide three examples of its use-calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.
Collapse
Affiliation(s)
- Eryk J Ratajczyk
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| |
Collapse
|
40
|
Abdolahzadeh A, Ang QR, Caine JR, Panchapakesan SSS, Thio S, Cojocaru R, Unrau PJ. Turn-on RNA Mango Beacons for trans-acting fluorogenic nucleic acid detection. RNA (NEW YORK, N.Y.) 2024; 30:392-403. [PMID: 38282417 PMCID: PMC10946430 DOI: 10.1261/rna.079833.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/03/2024] [Indexed: 01/30/2024]
Abstract
The Mango I and II RNA aptamers have been widely used in vivo and in vitro as genetically encodable fluorogenic markers that undergo large increases in fluorescence upon binding to their ligand, TO1-Biotin. However, while studying nucleic acid sequences, it is often desirable to have trans-acting probes that induce fluorescence upon binding to a target sequence. Here, we rationally design three types of light-up RNA Mango Beacons based on a minimized Mango core that induces fluorescence upon binding to a target RNA strand. Our first design is bimolecular in nature and uses a DNA inhibition strand to prevent folding of the Mango aptamer core until binding to a target RNA. Our second design is unimolecular in nature, and features hybridization arms flanking the core that inhibit G-quadruplex folding until refolding is triggered by binding to a target RNA strand. Our third design builds upon this structure, and incorporates a self-inhibiting domain into one of the flanking arms that deliberately binds to, and precludes folding of, the aptamer core until a target is bound. This design separates G-quadruplex folding inhibition and RNA target hybridization into separate modules, enabling a more universal unimolecular beacon design. All three Mango Beacons feature high contrasts and low costs when compared to conventional molecular beacons, with excellent potential for in vitro and in vivo applications.
Collapse
Affiliation(s)
- Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Quiana R Ang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Jana R Caine
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | | | - Shinta Thio
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| |
Collapse
|
41
|
Yao Y, Liu Y, Liu X, Zhang X, Shi P, Zhang X, Zhang Q, Wei X. Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios. iScience 2024; 27:109074. [PMID: 38361618 PMCID: PMC10867447 DOI: 10.1016/j.isci.2024.109074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
DNA tweezers, with their elegant simplicity and flexibility, have been pivotal in biosensing and DNA computing. However, conventional tweezers are confined to a binary transformation pre/post target signal recognition, limiting them to presence/absence judgments. This study introduces bubble DNA tweezers (BDT), capable of three distinct conformations based on variable target signal ratios. In contrast to traditional compact tweezers, BDT features a looser structure centered around a non-complementary bubble domain located between the tweezer arms' connecting axis and target signal recognition jaws. This bubble triggers toehold-free DNA strand displacement, leading to three conformational changes at different target signal concentrations. BDT detects presence/absence and true concentration with remarkable specificity and sensitivity. This adaptability is not confined to ideal scenarios, proving valuable in complex, noisy environments. Our method facilitates target DNA/miRNA signal quantification within a specific length range, promising applications in clinical research and environmental detection, while inspiring future biological assay innovations.
Collapse
Affiliation(s)
- Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| |
Collapse
|
42
|
Wu L, Wang GA, Li F. Plug-and-Play Module for Reversible and Continuous Control of DNA Strand Displacement Kinetics. J Am Chem Soc 2024; 146:6516-6521. [PMID: 38411013 DOI: 10.1021/jacs.3c09242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Regulatory modules for controlling the kinetics of toehold-mediated strand displacement (TMSD) play critical roles in designing dynamic and dissipative DNA chemical reaction networks (CRNs) but are hardwired into sequence designs. Herein, we introduce antitoehold (At), a plug-and-play module for reversible and continuous tuning of TMSD kinetics by temporarily occupying the toehold domain via a metastable duplex and base stacking. We demonstrate that kinetic control can be readily activated or deactivated in real time for any TMSD by simply adding At or anti-At. Continuous tuning of TMSD kinetics can also be achieved by altering the concentration of At. Moreover, the simple addition of At could readily reprogram existing TMSDs into a pulse-generation DNA CRN with continuous tunability. Our At approach also offers a new way for engineering continuously tunable DNA hybridization probes, which may find practical uses for discriminating clinically important mutations. Because of the simplicity, we anticipate that At will find wide applications for engineering DNA CRNs with diverse dynamic and dissipative behaviors, and DNA hybridization probes with tunable affinity and selectivity.
Collapse
Affiliation(s)
- Lang Wu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Guan A Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| |
Collapse
|
43
|
Nerantzaki M, Husser C, Ryckelynck M, Lutz JF. Exchanging and Releasing Information in Synthetic Digital Polymers Using a Strand-Displacement Strategy. J Am Chem Soc 2024; 146:6456-6460. [PMID: 38286022 DOI: 10.1021/jacs.3c13953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Toehold-mediated strand displacement (TMSD) was tested as a tool to edit information in synthetic digital polymers. Uniform DNA-polymer biohybrid macromolecules were first synthesized by automated phosphoramidite chemistry and characterized by HPLC, mass spectrometry, and polyacrylamide gel electrophoresis (PAGE). These precursors were diblock structures containing a synthetic poly(phosphodiester) (PPDE) segment covalently attached to a single-stranded DNA sequence. Three types of biohybrids were prepared herein: a substrate containing an accessible toehold as well as input and output macromolecules. The substrate and the input macromolecules contained noncoded PPDE homopolymers, whereas the output macromolecule contained a digitally encoded segment. After hybridization of the substrate with the output, incubation in the presence of the input led to efficient TMSD and the release of the digital segment. TMSD can therefore be used to erase or rewrite information in self-assembled biohybrid superstructures. Furthermore, it was found in this work that the conjugation of DNA single strands to synthetic segments of chosen lengths greatly facilitates the characterization and PAGE visualization of the TMSD process.
Collapse
Affiliation(s)
- Maria Nerantzaki
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Claire Husser
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| |
Collapse
|
44
|
Chen J, Dai Z, Lv H, Jin Z, Tang Y, Xie X, Shi J, Wang F, Li Q, Liu X, Fan C. Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification. Proc Natl Acad Sci U S A 2024; 121:e2312596121. [PMID: 38437555 PMCID: PMC10945798 DOI: 10.1073/pnas.2312596121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.
Collapse
Affiliation(s)
- Jielin Chen
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zheze Dai
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hui Lv
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
- Zhangjiang Laboratory, Shanghai201210, China
| | - Zhongchao Jin
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yuqing Tang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jiye Shi
- Division of Physical Biology, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai201800, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| |
Collapse
|
45
|
Huang WYC, Boxer SG, Ferrell JE. Membrane localization accelerates association under conditions relevant to cellular signaling. Proc Natl Acad Sci U S A 2024; 121:e2319491121. [PMID: 38427601 PMCID: PMC10927583 DOI: 10.1073/pnas.2319491121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024] Open
Abstract
Translocation of cytoplasmic molecules to the plasma membrane is commonplace in cell signaling. Membrane localization has been hypothesized to increase intermolecular association rates; however, it has also been argued that association should be faster in the cytosol because membrane diffusion is slow. Here, we directly compare an identical association reaction, the binding of complementary DNA strands, in solution and on supported membranes. The measured rate constants show that for a 10-µm-radius spherical cell, association is 22- to 33-fold faster at the membrane than in the cytoplasm. The kinetic advantage depends on cell size and is essentially negligible for typical ~1 µm prokaryotic cells. The rate enhancement is attributable to a combination of higher encounter rates in two dimensions and a higher reaction probability per encounter.
Collapse
Affiliation(s)
- William Y. C. Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - James E. Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| |
Collapse
|
46
|
Yang S, Bögels BWA, Wang F, Xu C, Dou H, Mann S, Fan C, de Greef TFA. DNA as a universal chemical substrate for computing and data storage. Nat Rev Chem 2024; 8:179-194. [PMID: 38337008 DOI: 10.1038/s41570-024-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.
Collapse
Affiliation(s)
- Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Can Xu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
| |
Collapse
|
47
|
Mallette TL, Lidke DS, Lakin MR. Heterochiral modifications enhance robustness and function of DNA in living human cells. Chembiochem 2024; 25:e202300755. [PMID: 38228506 PMCID: PMC10923132 DOI: 10.1002/cbic.202300755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
Oligonucleotide therapeutics are becoming increasingly important as more are approved by the FDA, both for treatment and vaccination. Similarly, dynamic DNA nanotechnology is a promising technique that can be used to sense exogenous input molecules or endogenous biomarkers and integrate the results of multiple sensing reactions in situ via a programmed cascade of reactions. The combination of these two technologies could be highly impactful in biomedicine by enabling smart oligonucleotide therapeutics that can autonomously sense and respond to a disease state. A particular challenge, however, is the limited lifetime of standard nucleic acid components in living cells and organisms due to degradation by endogenous nucleases. In this work, we address this challenge by incorporating mirror-image, ʟ-DNA nucleotides to produce heterochiral "gapmers". We use dynamic DNA nanotechnology to show that these modifications keep the oligonucleotide intact in living human cells for longer than an unmodified strand. To this end, we used a sequential transfection protocol for delivering multiple nucleic acids into living human cells while providing enhanced confidence that subsequent interactions are actually occurring within the cells. Taken together, this work advances the state of the art of ʟ-nucleic acid protection of oligonucleotides and DNA circuitry for applications in vivo.
Collapse
Affiliation(s)
- Tracy L Mallette
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, 87131, USA
| | - Diane S Lidke
- Department of Pathology and Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, 87131, USA
| | - Matthew R Lakin
- Department of Computer Science, Department of Chemical & Biological Engineering, Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, 87131, USA
| |
Collapse
|
48
|
Nakakuki T, Toyonari M, Aso K, Murayama K, Asanuma H, de Greef TFA. DNA Reaction System That Acquires Classical Conditioning. ACS Synth Biol 2024; 13:521-529. [PMID: 38279958 PMCID: PMC10877613 DOI: 10.1021/acssynbio.3c00459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/29/2024]
Abstract
Biochemical reaction networks can exhibit plastic adaptation to alter their functions in response to environmental changes. This capability is derived from the structure and dynamics of the reaction networks and the functionality of the biomolecule. This plastic adaptation in biochemical reaction systems is essentially related to memory and learning capabilities, which have been studied in DNA computing applications for the past decade. However, designing DNA reaction systems with memory and learning capabilities using the dynamic properties of biochemical reactions remains challenging. In this study, we propose a basic DNA reaction system design that acquires classical conditioning, a phenomenon underlying memory and learning, as a typical learning task. Our design is based on a simple mechanism of five DNA strand displacement reactions and two degradative reactions. The proposed DNA circuit can acquire or lose a new function under specific conditions, depending on the input history formed by repetitive stimuli, by exploiting the dynamic properties of biochemical reactions induced by different input timings.
Collapse
Affiliation(s)
- Takashi Nakakuki
- Department
of Intelligent and Control Systems, Faculty of Computer Science and
Systems Engineering, Kyushu Institute of
Technology 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan
| | - Masato Toyonari
- Department
of Intelligent and Control Systems, Faculty of Computer Science and
Systems Engineering, Kyushu Institute of
Technology 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan
| | - Kaori Aso
- Department
of Intelligent and Control Systems, Faculty of Computer Science and
Systems Engineering, Kyushu Institute of
Technology 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan
| | - Keiji Murayama
- Department
of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 4648603, Japan
| | - Hiroyuki Asanuma
- Department
of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 4648603, Japan
| | - Tom F. A. de Greef
- Laboratory
of Chemical Biology and Institute for Complex Molecular Systems and
Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, De Zaale, Eindhoven 5600 MB, The Netherlands
| |
Collapse
|
49
|
Zhang Y, Chen Y, Liu X, Ling Q, Wu R, Yang J, Zhang C. Programmable Primer Switching for Regulating Enzymatic DNA Circuits. ACS NANO 2024; 18:5089-5100. [PMID: 38286819 DOI: 10.1021/acsnano.3c12000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Developing DNA strand displacement reactions (SDRs) offers crucial technical support for regulating artificial nucleic acid circuits and networks. More recently, enzymatic SDR-based DNA circuits have gained significant attention because of their modular design, high orthogonality signaling, and extremely fast reaction rates. Typical enzymatic SDRs are regulated by relatively long primers (20-30 nucleotides) that hybridize to form stable double-stranded structures, facilitating enzyme-initiated events. Implementing more flexible primer-based enzymatic SDR regulations remains challenging due to the lack of convenient and simple primer control mechanism, which consequently limits the development of enzymatic DNA circuits. In this study, we propose an approach, termed primer switching regulation, that implements programmable and flexible regulations of enzymatic circuits by introducing switchable wires into the enzymatic circuits. We applied this method to generate diverse enzymatic DNA circuits, including cascading, fan-in/fan-out, dual-rail, feed-forward, and feedback functions. Through this method, complex circuit functions can be implemented by just introducing additional switching wires without reconstructing the basic circuit frameworks. The method is experimentally demonstrated to provide flexible and programmable regulations to control enzymatic DNA circuits and has future applications in DNA computing, biosensing, and DNA storage.
Collapse
Affiliation(s)
- Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Yiming Chen
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Xuan Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Qian Ling
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| |
Collapse
|
50
|
Ward EN, McClelland RM, Lamb JR, Rubio-Sánchez R, Christensen CN, Mazumder B, Kapsiani S, Mascheroni L, Di Michele L, Kaminski Schierle GS, Kaminski CF. Fast, multicolour optical sectioning over extended fields of view with patterned illumination and machine learning. BIOMEDICAL OPTICS EXPRESS 2024; 15:1074-1088. [PMID: 38404329 PMCID: PMC10890859 DOI: 10.1364/boe.510912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 02/27/2024]
Abstract
Structured illumination can reject out-of-focus signal from a sample, enabling high-speed and high-contrast imaging over large areas with widefield detection optics. However, this optical sectioning technique is currently limited by image reconstruction artefacts and poor performance at low signal-to-noise ratios. We combine multicolour interferometric pattern generation with machine learning to achieve high-contrast, real-time reconstruction of image data that is robust to background noise and sample motion. We validate the method in silico and demonstrate imaging of diverse specimens, from fixed and live biological samples to synthetic biosystems, reconstructing data live at 11 Hz across a 44 × 44μm2 field of view, and demonstrate image acquisition speeds exceeding 154 Hz.
Collapse
Affiliation(s)
- Edward N. Ward
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Rebecca M. McClelland
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Jacob R. Lamb
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Roger Rubio-Sánchez
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
- fabriCELL, Molecular Sciences Research Hub,
Imperial College London, London, W12 0BZ,
UK
| | - Charles N. Christensen
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Bismoy Mazumder
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Sofia Kapsiani
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Luca Mascheroni
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
- fabriCELL, Molecular Sciences Research Hub,
Imperial College London, London, W12 0BZ,
UK
| | | | - Clemens F. Kaminski
- Department of Chemical Engineering and
Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| |
Collapse
|