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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.
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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
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2
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Fu R, Hou J, Wang Z, Xianyu Y. DNA Molecular Computation Using the CRISPR-Mediated Reaction and Surface Growth of Gold Nanoparticles. ACS NANO 2024; 18:14754-14763. [PMID: 38781600 DOI: 10.1021/acsnano.4c04265] [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: 05/25/2024]
Abstract
DNA has emerged as a promising tool to build logic gates for biocomputing. However, prevailing methodologies predominantly rely on hybridization reactions or structural alterations to construct DNA logic gates, which are limited in simplicity and diversity. Herein, we developed simple and smart DNA-based logic gates for biocomputing through the DNA-mediated growth of gold nanomaterials without precise structure design and probe modification. Capitalizing on their excellent plasmonic properties, the surface growth of gold nanomaterials enables distinct wavelength shifts and unique shapes, which are modulated by the composition, length, and concentration of the DNA sequences. Combined with a CRISPR-mediated reaction, we constructed DNA circuits to achieve complicated biocomputing to modulate the surface growth of gold nanomaterials. By implementing logic functions controlled by input-mediated growth of gold nanomaterials, we established YES/NOT, AND/NAND, OR/NOR, XOR, and INHIBIT gates and further constructed cascade logic circuits, parity checker for natural numbers, and gray code encoder, which are promising for DNA biocomputing.
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Affiliation(s)
- Ruijie Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Jinjie Hou
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Zexiang Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
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3
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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] [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.
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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.
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Li C, Hu Y, Shi T, Dong K, Wu T. Label-free colorimetric detection platform based on catalytic hairpin self-assembly and G-quadruplex/hemin DNAzyme for comprehensive biomarker profiling. Talanta 2024; 272:125835. [PMID: 38422905 DOI: 10.1016/j.talanta.2024.125835] [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: 01/11/2024] [Revised: 02/22/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024]
Abstract
The expression level of human apurinic/apyrimidinic endonuclease 1 (APE1) is closely associated with the onset of various diseases, establishing it as a crucial clinical biomarker and a target in anti-cancer efforts. This study accomplished colorimetric and visual detection of APE1 by harnessing its endonuclease activity through catalytic hairpin self-assembly (CHA) and G-quadruplex/hemin DNAzyme. Optimization of the freedom degrees of the G-rich sequence significantly improved the detection performance of the strategy by influencing DNAzyme formation. Additionally, we replaced the signal reporting system with a molecular beacon to develop a fluorescence detection strategy, which served as an extension of the signal amplification system for validation and signal readout. The fluorescent probe method achieved a detection limit of 3.37 × 10-4 U/mL, while the colorimetric method yielded a detection limit of 6.5 × 10-3 U/mL, with a linear range spanning from 0.01 to 0.25 U/mL. Subsequently, the colorimetric approach effectively assessed APE1 activity in biological samples and facilitated the screening of APE1 activity inhibitors. Furthermore, this CHA/G-quadruplex/hemin DNAzyme strategy was adapted for the colorimetric detection of adenosine, showcasing its broad applicability across various biomarkers. The developed colorimetric analytical strategy represents a pivotal biosensing platform for diagnosing and treating diseases.
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Affiliation(s)
- Changjiang Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Tianzi Shi
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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5
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Ge W, Wang Y, Xiao SJ. Three-Point-Star Deoxyribonucleic Acid Tiles with the Core Arm Length at Three Half-Turns for Two-Dimensional Archimedean Tilings and Beyond. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10326-10333. [PMID: 38686650 DOI: 10.1021/acs.langmuir.4c00985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
2D Archimedean tiling and complex tessellation patterns assembled from soft materials including modular DNA tiles have attracted great interest because of their specific structures and potential applications in nanofabrication, nanoelectronics, nanophotonics, biomedical sensing, drug delivery, therapeutics, etc. Traditional three- and four-point-star DNA tiles with the core arm length at two half-turns (specified as three- and four-point-star-E previously and abbreviated as 3PSE and 4PSE tiles here) have been applied to assemble intricate tessellations through tuning the size of inserted nT (n = 1-7, T is thymine) loops on helper strands at the tile center. Following our recent findings using a new type of four-point-star tiles with the core arm length at three half-turns (specified as four-point-star-O previously and abbreviated as 4PSO tiles here) to assemble DNA tubes and flat 2D arrays, we report here the cross-hybridization weaving architectures at the tile center to construct three new 3PSO tiles with circular DNA oligonucleotides of 96-nt (nucleotides) serving as the scaffolds, further the monotonous and combinatory E- and O-tilings on one type of 3PSO tiles to create 2D Archimedean tiling patterns (6.6.6) and (4.8.8), and finally, the combination of 3PSO with 4PSO as well as 2PSO tiles to tile into complex tessellation patterns. The easy realization of regular and intricate DNA tessellations with 2-4PSO tiles not only richens the fundamental DNA modules and complex DNA nanostructures in types but also broadens the potential application scopes of DNA nanostructures in nanofabrication, DNA computing, biomedicine, etc.
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Affiliation(s)
- Wei Ge
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yantong Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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6
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Xiang Z, Zheng JY, Ma X, Chu Y, Song Q, Zhou G, Zou B, Wu H, Wang C. FEN1-assisted DNA logic amplifier circuit for fast and compact DNA computing. Chem Commun (Camb) 2024; 60:4593-4596. [PMID: 38577866 DOI: 10.1039/d4cc00203b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
This work developed DNA amplifier logic gates (AND-OR, OR-AND, FAN-IN, FAN-OUT, and 4-bit square-root circuits) using a flap endonuclease 1 (FEN1)-catalyzed signal amplification reaction, for the fastest and compact DNA computing. Moreover, the logic circuit can use input strands with concentrations of less than 1 nM, which is more than 100 times lower than the input concentration of other DNA logic circuits, providing a promising methodology for constructing fast and compact DNA computations.
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Affiliation(s)
- Zheng Xiang
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jia-Yi Zheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Xueping Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Yanan Chu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Qinxin Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Haiping Wu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Chen Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
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7
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Bardales AC, Vo Q, Kolpashchikov DM. Singleton {NOT} and Doubleton {YES; NOT} Gates Act as Functionally Complete Sets in DNA-Integrated Computational Circuits. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:600. [PMID: 38607134 PMCID: PMC11013093 DOI: 10.3390/nano14070600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
A functionally complete Boolean operator is sufficient for computational circuits of arbitrary complexity. We connected YES (buffer) with NOT (inverter) and two NOT four-way junction (4J) DNA gates to obtain IMPLY and NAND Boolean functions, respectively, each of which represents a functionally complete gate. The results show a technological path towards creating a DNA computational circuit of arbitrary complexity based on singleton NOT or a combination of NOT and YES gates, which is not possible in electronic computers. We, therefore, concluded that DNA-based circuits and molecular computation may offer opportunities unforeseen in electronics.
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Affiliation(s)
- Andrea C. Bardales
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA; (A.C.B.)
| | - Quynh Vo
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA; (A.C.B.)
| | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA; (A.C.B.)
- National Center for Forensic Sciences, University of Central Florida, Orlando, FL 32816, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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8
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Halužan Vasle A, Moškon M. Synthetic biological neural networks: From current implementations to future perspectives. Biosystems 2024; 237:105164. [PMID: 38402944 DOI: 10.1016/j.biosystems.2024.105164] [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: 06/14/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
Artificial neural networks, inspired by the biological networks of the human brain, have become game-changing computing models in modern computer science. Inspired by their wide scope of applications, synthetic biology strives to create their biological counterparts, which we denote synthetic biological neural networks (SYNBIONNs). Their use in the fields of medicine, biosensors, biotechnology, and many more shows great potential and presents exciting possibilities. So far, many different synthetic biological networks have been successfully constructed, however, SYNBIONN implementations have been sparse. The latter are mostly based on neural networks pretrained in silico and being heavily dependent on extensive human input. In this paper, we review current implementations and models of SYNBIONNs. We briefly present the biological platforms that show potential for designing and constructing perceptrons and/or multilayer SYNBIONNs. We explore their future possibilities along with the challenges that must be overcome to successfully implement a scalable in vivo biological neural network capable of online learning.
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Affiliation(s)
- Ana Halužan Vasle
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Moškon
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
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9
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Zhang L, Zhao H, Yang H, Su X. Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection. Biosens Bioelectron 2023; 239:115622. [PMID: 37611449 DOI: 10.1016/j.bios.2023.115622] [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: 05/29/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
DNA-based enzyme-free signal amplification strategies are widely employed to detect biomarkers in low abundance. To enhance signal amplification, localized DNA reaction units which increases molecular collision probability is commonly utilized. However, the current understanding of the structure-function relationships in localized DNA signal amplification probes is limited, leading to unsatisfied performance. In this study, we introduced a coarse-grained molecular model to simulate the dynamic behavior of two DNA reaction units within a DNA enzyme-free signal amplification circuit called Localized Catalytic Hairpin Assembly (LCHA). We investigated the impact of localized distance and flexibility on reaction performance. The most efficient LCHA probe guided by simulation exhibits sensitivity 28 times greater that of free CHA, with a detection limit of miR-21 reaching 16 pM, while the least effective LCHA probe demonstrated a modest improvement of only 7 times. We successfully employed the optimized probe to differentiate cancer cells from normal cells based on their miR-21 expression levels, showcasing its quantification ability. By elucidating the mechanistic insights and structure-function relationship in our work, we aim to contribute valuable information that can save users' time and reduce costs when designing localized DNA probes. With a comprehensive understanding of how the localization affects probe performance, researchers can now make more informed and efficient decisions during the design process. This work would find broad applications of DNA nanotechnology in biosensing, biocomputing, and bionic robots.
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Affiliation(s)
- Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hongyang Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huixiao Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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10
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Liu X, Li B, Liu Q, Zhang L, Zhao R, Wu D, Wang L, Wang Z, Xie G, Feng W. Multifunctional dumbbell probes-based logic circuits: microRNAs logic detection and tumor cells identification. Anal Chim Acta 2023; 1280:341856. [PMID: 37858550 DOI: 10.1016/j.aca.2023.341856] [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: 08/16/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND The powerful logic processing capability of DNA logic circuits over multiple input signals perfectly meets the demands of multi-biomarker-based clinical diagnostics. As important biomarkers for cancer diagnosis and treatment, the orthogonal differential expression of microRNAs (miRNAs) in different diseases and different cancer cells makes the precise logical detection of multiple miRNAs particularly critical. RESULTS Therefore, we constructed two fundamental "AND" and "OR" logic gates and one "AND-OR" logic gate on the basis of our proposed multifunctional dumbbell probes. These logic gates allowed for the logical profiling of multiple cancer-associated miRNAs. In addition, by making simple adjustments to the functional modules of multifunctional dumbbell probes, the three logic gates we proposed could be easily transformed without the use of sophisticated probe design. Remarkably, these logic gates, in particular the "AND-OR" logic gate, were able to compute several miRNAs simultaneously, demonstrating excellent cell identification capabilities. SIGNIFICANCE Overall, this work provided a new idea for accurately distinguishing multiple cell types and showed great application prospects.
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Affiliation(s)
- Xin Liu
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Baiying Li
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Qian Liu
- Department of Nuclear Medicine, The Second Hospital of Chongqing Medical University, Chongqing 400010, PR China
| | - Li Zhang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Di Wu
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China.
| | - Wenli Feng
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China.
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11
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Zhang C, Paluzzi VE, Sha R, Jonoska N, Mao C. Implementing Logic Gates by DNA Crystal Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302345. [PMID: 37220213 DOI: 10.1002/adma.202302345] [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: 03/13/2023] [Revised: 05/03/2023] [Indexed: 05/25/2023]
Abstract
DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Natasha Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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12
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Liu J, Liu S, Zou C, Xu S, Zhou C. Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates. IEEE Trans Nanobioscience 2023; 22:245-258. [PMID: 35679378 DOI: 10.1109/tnb.2022.3181615] [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: 11/05/2022]
Abstract
As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.
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13
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Meng F, Yu W, Niu M, Tian X, Miao Y, Li X, Zhou Y, Ma L, Zhang X, Qian K, Yu Y, Wang J, Huang L. Ratiometric electrochemical OR gate assay for NSCLC-derived exosomes. J Nanobiotechnology 2023; 21:104. [PMID: 36964516 PMCID: PMC10037838 DOI: 10.1186/s12951-023-01833-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/26/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common pathological type of LC and ranks as the leading cause of cancer deaths. Circulating exosomes have emerged as a valuable biomarker for the diagnosis of NSCLC, while the performance of current electrochemical assays for exosome detection is constrained by unsatisfactory sensitivity and specificity. Here we integrated a ratiometric biosensor with an OR logic gate to form an assay for surface protein profiling of exosomes from clinical serum samples. By using the specific aptamers for recognition of clinically validated biomarkers (EpCAM and CEA), the assay enabled ultrasensitive detection of trace levels of NSCLC-derived exosomes in complex serum samples (15.1 particles μL-1 within a linear range of 102-108 particles μL-1). The assay outperformed the analysis of six serum biomarkers for the accurate diagnosis, staging, and prognosis of NSCLC, displaying a diagnostic sensitivity of 93.3% even at an early stage (Stage I). The assay provides an advanced tool for exosome quantification and facilitates exosome-based liquid biopsies for cancer management in clinics.
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Affiliation(s)
- Fanyu Meng
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Wenjun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Minjia Niu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xvelian Li
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yan Zhou
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yongchun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
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14
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Wang Y, Wang L, Hu W, Qian M, Dong Y. Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation. Interdiscip Sci 2023; 15:1-14. [PMID: 36763314 DOI: 10.1007/s12539-023-00551-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 02/11/2023]
Abstract
As a well-established technique, DNA synthesis offers interesting possibilities for designing multifunctional nanodevices. The micro-processing system of modern semiconductor circuits is dependent on strategies organized on silicon chips to achieve the speedy transmission of substances or information. Similarly, spatially localized structures allow for fixed DNA molecules in close proximity to each other during the synthesis of molecular circuits, thus providing a different strategy that of opening up a remarkable new area of inquiry for researchers. Herein, the Visual DSD (DNA strand displacement) modeling language was used to design and analyze the spatially organized DNA reaction network. The execution rules depend on the hybridization reaction caused by directional complementary nucleotide sequences. A series of DNA strand displacement calculations were organized on the locally coded travel track, and autonomous movement and addressing operations are gradually realized. The DNA nanodevice operates in this manner follows the embedded "molecular program", which improves the reusability and scalability of the same sequence domain in different contexts. Through the communication between various building blocks, the DNA device-carrying the target molecule moves in a controlled manner along the programmed track. In this way, a variety of molecular functional group transport and specific partition storage can be realized. The simulation results of the visual DSD tool provide qualitative and quantitative proof for the operation of the system.
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Affiliation(s)
- Yue Wang
- School of Life Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.,Department of Information Engineering, Taiyuan City Vocational and Technical College, Taiyuan, 030027, Shanxi, China
| | - Luhui Wang
- School of Life Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Wenxiao Hu
- School of Life Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Mengyao Qian
- School of Life Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Yafei Dong
- School of Life Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.
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15
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Mao C, Wang S, Li J, Feng Z, Zhang T, Wang R, Fan C, Jiang X. Metal-Organic Frameworks in Microfluidics Enable Fast Encapsulation/Extraction of DNA for Automated and Integrated Data Storage. ACS NANO 2023; 17:2840-2850. [PMID: 36728704 DOI: 10.1021/acsnano.2c11241] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
DNA as an exceptional data storage medium offers high information density. However, DNA storage requires specialized equipment and tightly controlled environments for storage. Fast encapsulation within minutes for enhanced DNA stability to do away with specialized equipment and fast DNA extraction remain a challenge. Here, we report a DNA microlibrary that can be encapsulated by metal-organic frameworks (MOFs) within 10 min and extracted (5 min) in a single microfluidic chip for automated and integrated DNA-based data storage. The DNA microlibrary@MOFs enhances the stability of data-encoded DNA against harsh environments. The encoded information can be read out perfectly after accelerated aging, equivalent to being readable after 10 years of storage at 25 °C, 50% relative humidity, and 10 000 lx sunlight radiation. Moreover, the library enables fast retrieval of target data via flow cytometry and can be reproduced after each access.
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Affiliation(s)
- Cuiping Mao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Shuchen Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Jiankai Li
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Zhuowei Feng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Tong Zhang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Rui Wang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Chunhai Fan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, No 800, DongChuan Road, Minhang District, Shanghai 200240, People's Republic of China
| | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
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16
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Li S, Wang Y, Ge W, Zhang W, Lu B, Feng F, Ni C, Xiao SJ. Tuning the Roundabout of Four-Point-Star Tiles with the Core Arm Length of Three Half-Turns for 2D DNA Arrays. Chemistry 2023; 29:e202202863. [PMID: 36251733 DOI: 10.1002/chem.202202863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Indexed: 11/05/2022]
Abstract
By rationally adjusting the weaving modes of point-star tiles, the curvature inherent in the tiles can be changed, and various DNA nanostructures can be assembled, such as planar wireframe meshes, perforated wireframe tubes, and curved wireframe polyhedra. Based on the weaving and tiling architectures for traditional point-star tiles with the core arm length at two DNA half-turns, we improved the weaving modes of our newly reported four-point-star tiles with the core arm length at three half-turns to adjust their curvature and rigidity for assembling 2D arrays of DNA grids and tubes. Following our previous terms and methods to analyze the structural details of E-tiling tubes, we used the chiral indices (n,m) to describe the most abundant tube of typical assemblies; especially, we applied both one-locus and/or dual-locus biotin/streptavidin (SA) labelling strategies to define the configurations of two specific tubes, along with the absolute conformations of their component tiles. Such structural details of the DNA tubes composed of tiles with addressable concave and convex faces and packing directions should help us understand their physio-chemical and biological properties, and therefore promote their applications in drug delivery, biocatalysis, biomedicine, etc.
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Affiliation(s)
- Shijie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Yantong Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Wei Ge
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Wei Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Biao Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Caihong Ni
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
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17
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Liao Y, Hu H, Tang X, Qin Y, Zhang W, Dong K, Yan B, Mu Y, Li L, Ming Z, Xiao X. A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices. Nucleic Acids Res 2022; 51:29-40. [PMID: 36537218 PMCID: PMC9841412 DOI: 10.1093/nar/gkac1193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/18/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Toehold-mediated strand displacement and its regulatory tools are fundamental for DNA nanotechnology. However, current regulatory tools all need to change the original sequence of reactants, making the regulation inconvenient and cumbersome. More importantly, the booming development of DNA nanotechnology will soon promote the production of packaged and batched devices or circuits with specified functions. Regarding standardized, packaged DNA nanodevices, access to personalized post-modification will greatly help users, whereas none of the current regulatory tools can provide such access, which has greatly constrained DNA nanodevices from becoming more powerful and practical. Herein, we developed a novel regulation tool named Cap which has two basic functions of subtle regulation of the reaction rate and erasability. Based on these functions, we further developed three advanced functions. Through integration of all functions of Cap and its distinct advantage of working independently, we finally realized personalized tailor-made post-modification on pre-fabricated DNA circuits. A pre-fabricated dual-output DNA circuit was successfully transformed into an equal-output circuit, a signal-antagonist circuit and a covariant circuit according to our requirements. Taken together, Cap is easy to design and generalizable for all strand displacement-based DNA nanodevices. We believe the Cap tool will be widely used in regulating reaction networks and personalized tailor-made post-modification of DNA nanodevices.
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Affiliation(s)
| | | | | | - Yang Qin
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kejun Dong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yaoqin Mu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Longjie Li
- Correspondence may also be addressed to Longjie Li.
| | - Zhihao Ming
- Correspondence may also be addressed to Zhihao Ming.
| | - Xianjin Xiao
- To whom correspondence should be addressed. Tel: +86 027 8369 2651; Fax: +86 027 8369 2651;
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18
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Chen C, Chen X, Li X, Shi X. DNA computing for gastric cancer analysis and functional classification. Front Genet 2022; 13:1064715. [PMID: 36506309 PMCID: PMC9729876 DOI: 10.3389/fgene.2022.1064715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022] Open
Abstract
Early identification of key biomarkers of malignant cancer is vital for patients' prognosis and therapies. There is research demonstrating that microRNAs are important biomarkers for cancer analysis. In this article, we used the DNA strand displacement mechanism (DSD) to construct the DNA computing system for cancer analysis. First, gene chips were obtained through bioinformatical training. These microRNA data and clinical traits were obtained from the Cancer Genome Atlas (TCGA) dataset. Second, we analyzed the expression data by using a weighted gene co-expression network (WGCNA) and found four biomarkers for two clinic features, respectively. Last, we constructed a DSD-based DNA computing system for cancer analysis. The inputs of the system are these identified biomarkers; the outputs are the fluorescent signals that represent their corresponding traits. The experiment and simulation results demonstrated the reliability of the DNA computing system. This DSD simulation system is lab-free but clinically meaningful. We expect this innovative method to be useful for rapid and accurate cancer diagnosis.
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Affiliation(s)
- Congzhou Chen
- School of Computer Science, Peking University, Beijing, China
| | - Xin Chen
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Xin Li
- Department Genecology 2, Renmin Hospital of Wuhan University, Wuhan, China,*Correspondence: Xin Li, ; Xiaolong Shi,
| | - Xiaolong Shi
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China,*Correspondence: Xin Li, ; Xiaolong Shi,
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19
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Doricchi A, Platnich CM, Gimpel A, Horn F, Earle M, Lanzavecchia G, Cortajarena AL, Liz-Marzán LM, Liu N, Heckel R, Grass RN, Krahne R, Keyser UF, Garoli D. Emerging Approaches to DNA Data Storage: Challenges and Prospects. ACS NANO 2022; 16:17552-17571. [PMID: 36256971 PMCID: PMC9706676 DOI: 10.1021/acsnano.2c06748] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 1014 GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 103 GB/mm3. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.
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Affiliation(s)
- Andrea Doricchi
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università
di Genova, via Dodecaneso
31, 16146 Genova, Italy
| | - Casey M. Platnich
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Andreas Gimpel
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Friederikee Horn
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Max Earle
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - German Lanzavecchia
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Aitziber L. Cortajarena
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
| | - Luis M. Liz-Marzán
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Av. Monforte de Lemos, 3-5. Pabellón 11.
Planta 0, 28029 Madrid, Spain
| | - Na Liu
- Second
Physics Institute, University of Stuttgart, 70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, 70569 Stuttgart, Germany
| | - Reinhard Heckel
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Robert N. Grass
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
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20
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Majikes JM, Liddle JA. Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology. NANOSCALE 2022; 14:15586-15595. [PMID: 36268635 PMCID: PMC10949957 DOI: 10.1039/d2nr04040a] [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] [Indexed: 06/16/2023]
Abstract
Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications. For the last 20 years, it has been suggested that NAN might be an effective replacement for parts of the semiconductor lithography or protein engineering workflows. However, in that time, these incumbent technologies have made significant advances, and our understanding of NAN's strengths and weaknesses has progressed, suggesting that the greatest opportunities in fact lie elsewhere. Given the commitment of resources necessary to bring new technologies to the market and the desire to use those resources as wisely as possible, we conduct a critical examination of where NAN may benefit from, and provide benefit to, adjacent technologies and compete least with market incumbents. While the accuracy of our conclusions may be limited by our ability to extrapolate from the current state of NAN to its future commercial success, we conclude that the next promising direction is to create a bridge between biology and semiconductor technology. We also hope to stimulate a robust conversation around this technology's capabilities with the goal of building consensus on those research and development efforts that would advance NAN to the greatest effect in real-world applications.
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Affiliation(s)
- Jacob M Majikes
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
| | - J Alexander Liddle
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
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21
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Deng W, Xu JY, Peng H, Huang CZ, Le XC, Zhang H. DNAzyme motor systems and logic gates facilitated by toehold exchange translators. Biosens Bioelectron 2022; 217:114704. [PMID: 36113301 DOI: 10.1016/j.bios.2022.114704] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
DNAzyme motor systems using gold nanoparticles (AuNPs) as scaffolds are useful for biosensing and in situ amplification because these systems are free of protein enzymes, isothermal, homogeneous, and sensitive. However, detecting different targets using the available DNAzyme motor techniques requires redesigns of the DNAzyme motor. We report here a toehold-exchange translator and the translator-mediated DNAzyme motor systems, which enable sensitive responses to various nucleic acid targets using the same DNAzyme motor without requiring redesign. The translator is able to efficiently convert different nucleic acid targets into a specific output DNA that further activates the pre-silenced DNAzyme motor and consequently initiates the autonomous walking of the DNAzyme motor. Simply adjusting the target-binding region of the translator enables the same DNAzyme motor system to respond to various nucleic acid targets. The translator-mediated DNAzyme motor system is able to detect as low as 2.5 pM microRNA-10b and microRNA-21 under room temperature without the need of separation or washing. We further demonstrate the versatility of the translator and the DNAzyme motor by successful construction and operation of four logic gates, including OR, AND, NOR, and NAND logic gates. These logic gates use two microRNA targets as inputs and generate amplified fluorescence signals from the operation of the same DNAzyme motor. Incorporation of the toehold-exchange translator into the DNAzyme motor technology improves the biosensing applications of DNA motors to diverse nucleic acid targets.
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Affiliation(s)
- Wenchan Deng
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada; College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Jing Yang Xu
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hanyong Peng
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Cheng Zhi Huang
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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22
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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23
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Liu X, Zhang Q, Zhang X, Liu Y, Yao Y, Kasabov N. Construction of Multiple Logic Circuits Based on Allosteric DNAzymes. Biomolecules 2022; 12:biom12040495. [PMID: 35454084 PMCID: PMC9032175 DOI: 10.3390/biom12040495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
In DNA computing, the implementation of complex and stable logic operations in a universal system is a critical challenge. It is necessary to develop a system with complex logic functions based on a simple mechanism. Here, the strategy to control the secondary structure of assembled DNAzymes’ conserved domain is adopted to regulate the activity of DNAzymes and avoid the generation of four-way junctions, and makes it possible to implement basic logic gates and their cascade circuits in the same system. In addition, the purpose of threshold control achieved by the allosteric secondary structure implements a three-input DNA voter with one-vote veto function. The scalability of the system can be remarkably improved by adjusting the threshold to implement a DNA voter with 2n + 1 inputs. The proposed strategy provides a feasible idea for constructing more complex DNA circuits and a highly integrated computing system.
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Affiliation(s)
- Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
- Correspondence: ; Tel.: +86-0411-84708470
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Nikola Kasabov
- Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland 1010, New Zealand;
- Intelligent Systems Research Center, Ulster University, Londonderry BT52 1SA, UK
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24
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A high-integrated DNA biocomputing platform for MicroRNA sensing in living cells. Biosens Bioelectron 2022; 207:114183. [PMID: 35303538 DOI: 10.1016/j.bios.2022.114183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/31/2022]
Abstract
DNA logic computing has captured increasing interest due to its ability to assemble programmable DNA computing elements for disease diagnosis, gene regulation, and targeted therapy. In this work, we developed an aptamer-equipped high-integrated DNA biocomputing platform (HIDBP-A) with a dual-recognition function that enabled cancer cell targeting. Dual microRNAs were the input signals and can perform AND logic operations. Compared to the free DNA biocomputing platform (FDBP), the integration of all computing elements into the same DNA tetrahedron greatly improved logic computing speed and efficiency owing to the confinement effect reflected by the high local concentration of computing elements. As a proof of concept, the utilization of microRNA as the input signal was beneficial for improving the scalability and flexibility of the sequence design of the logic nano-platform. Given that the different microRNAs were over-expressed in cancer cells, this new HIDBP-A has great promise in accurate diagnosis and logic-controlled disease treatment.
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25
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Chen L, Chen W, Liu G, Li J, Lu C, Li J, Tan W, Yang H. Nucleic acid-based molecular computation heads towards cellular applications. Chem Soc Rev 2021; 50:12551-12575. [PMID: 34604889 DOI: 10.1039/d0cs01508c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids, with the advantages of programmability and biocompatibility, have been widely used to design different kinds of novel biocomputing devices. Recently, nucleic acid-based molecular computing has shown promise in making the leap from the test tube to the cell. Such molecular computing can perform logic analysis within the confines of the cellular milieu with programmable modulation of biological functions at the molecular level. In this review, we summarize the development of nucleic acid-based biocomputing devices that are rationally designed and chemically synthesized, highlighting the ability of nucleic acid-based molecular computing to achieve cellular applications in sensing, imaging, biomedicine, and bioengineering. Then we discuss the future challenges and opportunities for cellular and in vivo applications. We expect this review to inspire innovative work on constructing nucleic acid-based biocomputing to achieve the goal of precisely rewiring, even reconstructing cellular signal networks in a prescribed way.
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Affiliation(s)
- Lanlan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Wanzhen Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Guo Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Jingying Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China. .,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Weihong Tan
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
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26
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Xu C, Ma B, Gao Z, Dong X, Zhao C, Liu H. Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage. SCIENCE ADVANCES 2021; 7:eabk0100. [PMID: 34767438 PMCID: PMC8589306 DOI: 10.1126/sciadv.abk0100] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
DNA has been considered as a compelling candidate for digital data storage due to advantages such as high coding density, long retention time, and low energy consumption. Despite many works reported, the development of a DNA-based database of full integration, high efficiency, and practical applicability is still challenging. In this work, we report the synthesis and sequencing of DNA on a single electrode with scalability for an integrated DNA-based data storage system. The synthesis of DNA is based on phosphoramidite chemistry and electrochemical deprotection. The sequencing relies on charge redistribution originated from polymerase-catalyzed primer extension, leading to a measurable current spike. By regeneration of the electrode after sequencing, repeated sequencing can be achieved to improve the accuracy. A SlipChip device is developed to simplify the liquid introduction involved in DNA synthesis and sequencing. As the proof-of-concept experiment, text information is stored in the system and then accurately retrieved.
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27
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Zhu L, Yu L, Yang X. Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:42250-42257. [PMID: 34452580 DOI: 10.1021/acsami.1c12650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.
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Affiliation(s)
- Liping Zhu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Linying Yu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Xiurong Yang
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
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28
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Abstract
DNA-based Boolean logic gates (for example, AND, OR, and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. By utilizing photocaging groups, we developed a novel DNA gate design that prevents gate function until irradiation at a certain time point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all other components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA sequences. We further demonstrate the utility of the NOT gate within multilayer circuits in response to a specific pattern of four microRNAs.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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29
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Abe K, Murata S, Kawamata I. Cascaded pattern formation in hydrogel medium using the polymerisation approach. SOFT MATTER 2021; 17:6160-6167. [PMID: 34085082 DOI: 10.1039/d1sm00296a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Reaction-diffusion systems are one of the models of the formation process with various patterns found in nature. Inspired by natural pattern formation, several methods for designing artificial chemical reaction-diffusion systems have been proposed. DNA is a suitable building block to build such artificial systems owing to its programmability. Previously, we reported a line pattern formed due to the reaction and diffusion of synthetic DNA; however, the width of the line was too wide to be used for further applications such as parallel and multi-stage pattern formations. Here, we propose a novel method to programme a reaction-diffusion system in a hydrogel medium to realise a sharp line capable of forming superimposed and cascaded patterns. The mechanism of this system utilises a two-segment polymerisation of DNA caused by hybridisation. To superimpose the system, we designed orthogonal DNA sequences that formed two lines in different locations on the hydrogel. Additionally, we designed a reaction to release DNA and form a cascade pattern, in which the third line appears between the two lines. To explain the mechanism of our system, we modelled the system as partial differential equations, whose simulation results agreed well with the experimental data. Our method to fabricate cascaded patterns may inspire combinations of DNA-based technologies and expand the applications of artificial reaction-diffusion systems.
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Affiliation(s)
- Keita Abe
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan.
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan.
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan. and Natural Science Division, Faculty of Core Research, Ochanomizu University, Japan
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30
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Fan Z, Yao B, Ding Y, Xie M, Zhao J, Zhang K, Huang W. Electrochemiluminescence aptasensor for Siglec-5 detection based on MoS 2@Au nanocomposites emitter and exonuclease III-powered DNA walker. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 334:129592. [PMID: 33584010 PMCID: PMC7869706 DOI: 10.1016/j.snb.2021.129592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 05/03/2023]
Abstract
Lectins are highly specific binding proteins for glycoproteins which widely exist in living organisms, playing a vital role in exploring the biological evolution process, such as cellular proliferation, differentiation, carcinogenesis and apoptosis. Therefore, the content monitoring of lectin becomes particularly significant and urgent in the bioanalytical application. In this work, we fabricated an aptasensor, majorly capitalizing the eminent affinity between sialic acid-binding immunoglobulin (Ig)-like lectin 5 (Siglec-5) and nucleic acids aptamer (K19), with nontoxic MoS2@Au nanocomposites as electrochemiluminescence (ECL) emitters based on exonuclease III (Exo III)-powered DNA walker for the bioassays of Siglec-5. The DNA track was constructed on the emitters' surface, providing a reliable platform for the DNA walker's autonomous move. In the assay, the primer DNA in the DNA duplex was replaced by Siglec-5 due to the aptamer interactions and repeatedly released to participate in the movement of the DNA walker, further triggering cascade signal amplification. Finally, our aptasensor indicates significant potential for assays of Siglec-5 with a detection limit of 8.9 pM.
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Affiliation(s)
- Zhenqiang Fan
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, China
| | - Bo Yao
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, China
| | - Yuedi Ding
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Minhao Xie
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Jianfeng Zhao
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, China
| | - Kai Zhang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, China
- Shaanxi Institute of Flexible Electronics (SIFE), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, 710072, Shaanxi, China
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31
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Zhao S, Yu L, Yang S, Tang X, Chang K, Chen M. Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies. NANOSCALE HORIZONS 2021; 6:298-310. [PMID: 33877218 DOI: 10.1039/d0nh00587h] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.
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Affiliation(s)
- Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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32
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Zhou Z, Wang J, Levine RD, Remacle F, Willner I. DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations. Chem Sci 2021; 12:5473-5483. [PMID: 34168788 PMCID: PMC8179666 DOI: 10.1039/d1sc01098k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 11/21/2022] Open
Abstract
A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.
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Affiliation(s)
- Zhixin Zhou
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Jianbang Wang
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - R D Levine
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Francoise Remacle
- Theoretical Physical Chemistry, UR MolSys B6c, University of Liège B4000 Liège Belgium
| | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
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33
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Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:molecules26061502. [PMID: 33801952 PMCID: PMC8000633 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
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34
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Watson EE, Angerani S, Sabale PM, Winssinger N. Biosupramolecular Systems: Integrating Cues into Responses. J Am Chem Soc 2021; 143:4467-4482. [DOI: 10.1021/jacs.0c12970] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Emma E. Watson
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Simona Angerani
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M. Sabale
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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35
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Luo T, Fan S, Liu Y, Song J. Information processing based on DNA toehold-mediated strand displacement (TMSD) reaction. NANOSCALE 2021; 13:2100-2112. [PMID: 33475669 DOI: 10.1039/d0nr07865d] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
SemiSynBio is an emerging topic toward the construction of platforms for next-generation information processing. Recent research has indicated its promising prospect toward information processing including algorithm design and pattern manipulation with the DNA TMSD reaction, which is one of the cores of the SemiSynBio technology route. The DNA TMSD reaction is the process in which an invader strand displaces the incumbent strand from the gate strand through initiation at the exposed toehold domain. Also, the DNA TMSD reaction generally involves three processes: toehold association, branch migration and strand disassociation. Herein, we review the recent progress on information processing with the DNA TMSD reaction. We highlight the diverse developments on information processing with the logic circuit, analog circuit, combinational circuit and information relay with the DNA origami structure. Additionally, we explore the current challenges and various trends toward the design and application of the DNA TMSD reaction in future information processing.
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Affiliation(s)
- Tao Luo
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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36
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Lim CK, Nirantar S, Yew WS, Poh CL. Novel Modalities in DNA Data Storage. Trends Biotechnol 2021; 39:990-1003. [PMID: 33455842 DOI: 10.1016/j.tibtech.2020.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this paradigm include the cost of DNA synthesis and sequencing, along with low throughput. Further unresolved questions include the appropriate media of storage and the scalability of such approaches for commercial viability. In this review, we examine various storage modalities involving the use of DNA from a systems-level perspective. We compare novel methods that draw inspiration from molecular biology techniques that have been devised to overcome the difficulties posed by standard workflows and conceptualize potential applications that can arise from these advances.
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Affiliation(s)
- Cheng Kai Lim
- NUS Graduate School of Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore
| | | | - Wen Shan Yew
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore.
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37
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Hao Y, Li J, Li Q, Zhang L, Shi J, Zhang X, Aldalbahi A, Wang L, Fan C, Wang F. Programmable Live-Cell CRISPR Imaging with Toehold-Switch-Mediated Strand Displacement. Angew Chem Int Ed Engl 2020; 59:20612-20618. [PMID: 32744433 DOI: 10.1002/anie.202009062] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/14/2022]
Abstract
The widespread application of CRISPR-Cas9 has transformed genome engineering. Nevertheless, the precision to control the targeting activity of Cas9 requires further improvement. We report a toehold-switch-based approach to engineer the conformation of single guide RNA (sgRNA) for programmable activation of Cas9. This activation circuit is responsive to multiple inputs and can regulate the conformation of the sgRNA through toehold-switch-mediated strand displacement. We demonstrate the orthogonal suppression and activation of Cas9 with orthogonal DNA inputs. Combination of toehold switches leads to a variety of intracellular Cas9 activation programs with simultaneous and orthogonal responses, through which multiple genome loci are displayed in different colors in a controllable manner. This approach provides a new route for programing CRISPR in living cells for genome imaging and engineering.
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Affiliation(s)
- Yaya Hao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiang Li
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Luhao Zhang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xueli Zhang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Southern Medical University, Affiliated Fengxian Hospital, Shanghai, 201499, China
| | - Ali Aldalbahi
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Lihua Wang
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Southern Medical University, Affiliated Fengxian Hospital, Shanghai, 201499, China
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38
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Hao Y, Li J, Li Q, Zhang L, Shi J, Zhang X, Aldalbahi A, Wang L, Fan C, Wang F. Programmable Live‐Cell CRISPR Imaging with Toehold‐Switch‐Mediated Strand Displacement. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yaya Hao
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiang Li
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Luhao Zhang
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Jiye Shi
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Xueli Zhang
- Joint Research Center for Precision Medicine Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus Southern Medical University Affiliated Fengxian Hospital Shanghai 201499 China
| | - Ali Aldalbahi
- Department of Chemistry College of Science King Saud University Riyadh 11451 Saudi Arabia
| | - Lihua Wang
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Molecular Medicine, Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
- Joint Research Center for Precision Medicine Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus Southern Medical University Affiliated Fengxian Hospital Shanghai 201499 China
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39
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Lv M, Zhou W, Fan D, Guo Y, Zhu X, Ren J, Wang E. Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA-Templated Silver Nanoclusters as Universal Dual-Output Generators. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1908480. [PMID: 32196133 DOI: 10.1002/adma.201908480] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 05/21/2023]
Abstract
Exquisite administration of a new type of hairpin DNA-templated silver nanoclusters (H-AgNCs) as universal dual-output generators in DNA-based logic systems is reported. Diverse concomitant contrary logic gates (CCLGs) with opposite functions (YES^ NOT, OR^ NOR, INHIBIT^ IMPLICATION, XOR^ XNOR, and MAJORITY^ MINORITY) and extended concatenated logic circuits are presented and some of them perform specific functions, such as parity generators and checkers. The introduction of H-AgNCs as noncovalent signal reporters avoids tedious and high-cost labeling procedures. Of note, the concomitant feature of CCLGs attributed to the dual-emitter AgNCs conduces to reducing the time and cost to devise multiple logic gates. As compared to previous ones, this design eliminates numerous substances (e.g., organic dyes) and unstable components (hydrogen peroxide), which not only decreases the complexity of logic performs and improves repeatability of operation, but also makes it convenient to connect distinct DNA-based logic gates. It is worthy to anticipate that the cost-effective strategy will inspire researchers to develop much more complex logic systems and contribute to the field of molecular computing.
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Affiliation(s)
- Mengmeng Lv
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weijun Zhou
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Daoqing Fan
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yuchun Guo
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
| | - Xiaoqing Zhu
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jiangtao Ren
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Erkang Wang
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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40
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Implementing digital computing with DNA-based switching circuits. Nat Commun 2020; 11:121. [PMID: 31913309 PMCID: PMC6949259 DOI: 10.1038/s41467-019-13980-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/09/2019] [Indexed: 11/30/2022] Open
Abstract
DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. Switching circuits that were originally proposed by Shannon in 1938 and nowadays widely used in telecommunication represent an alternative and efficient means to realize fast-speed and high-bandwidth communication. Here we develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. We further demonstrate the implementation of full-adder and square-rooting functions using DSCs, which only uses down to 1/4 DNA strands as compared with a dual-rail logic expression-based design. We expect that DSCs provide a design paradigm for digital computation with biomolecules. DNA strand displacement reactions can be difficult to scale up for computational tasks. Here the authors develop DNA switching circuits that achieve high-speed computing with fewer molecules.
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41
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Demuth J, Miletin M, Kucera R, Ruzicka A, Havlinova Z, Libra A, Novakova V, Zimcik P. Self-assembly of azaphthalocyanine–oligodeoxynucleotide conjugates into J-dimers: towards biomolecular logic gates. Org Chem Front 2020. [DOI: 10.1039/c9qo01364d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Unique spatial self-assembly of azaphthalocyanine–oligonucleotide–fluorescein conjugates can be selectively dissociated by a complementary sequence or coordinating solvent and used for the development of biomolecular logic gates.
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Affiliation(s)
- Jiri Demuth
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Radim Kucera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Ales Ruzicka
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- Pardubice
- Czech Republic
| | - Zuzana Havlinova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | | | - Veronika Novakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
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