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Zhao T, Xiao R, Li Y, Ren J, Niu L, Chang B. An Exo III-powered closed-loop DNA circuit architecture for biosensing/imaging. Mikrochim Acta 2024; 191:395. [PMID: 38877347 DOI: 10.1007/s00604-024-06476-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
With their regulated Boolean logic operations in vitro and in vivo, DNA logic circuits have shown great promise for target recognition and disease diagnosis. However, significant obstacles must be overcome to improve their operational efficiency and broaden their range of applications. In this study, we propose an Exo III-powered closed-loop DNA circuit (ECDC) architecture that integrates four highly efficient AND logic gates. The ECDC utilizes Exo III as the sole enzyme-activated actuator, simplifying the circuit design and ensuring optimal performance. Moreover, the use of Exo III enables a self-feedback (autocatalytic) mechanism in the dynamic switching between AND logic gates within this circulating logic circuit. After validating the signal flow and examining the impact of each AND logic gate on the regulation of the circuit, we demonstrate the intelligent determination of miR-21 using the carefully designed ECDC architecture in vitro. The proposed ECDC exhibits a linear detection range for miR-21 from 0 to 300 nM, with a limit of detection (LOD) of approximately 0.01 nM, surpassing most reported methods. It also shows excellent selectivity for miR-21 detection and holds potential for identifying and imaging live cancer cells. This study presents a practical and efficient strategy for monitoring various nucleic acid-based biomarkers in vitro and in vivo through specific sequence modifications, offering significant potential for early cancer diagnosis, bioanalysis, and prognostic clinical applications.
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Affiliation(s)
- Tangtang Zhao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, 56 Xinjian South Road, Taiyuan, 030000, Shanxi, P.R. China
| | - Ruilin Xiao
- College of Safety and Emergency Management and Engineering, Taiyuan University of Technology, Taiyuan, 030000, Shanxi, China
| | - Yueqi Li
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, 56 Xinjian South Road, Taiyuan, 030000, Shanxi, P.R. China
| | - Jierong Ren
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, 56 Xinjian South Road, Taiyuan, 030000, Shanxi, P.R. China
| | - Liyun Niu
- Department of Colorectal and Anal Surgery, Shanxi Provincial People's Hospital, Taiyuan, 030000, Shanxi, China
| | - Bingmei Chang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, 56 Xinjian South Road, Taiyuan, 030000, Shanxi, P.R. China.
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2
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Bardales AC, Smirnov V, Taylor K, Kolpashchikov DM. DNA Logic Gates Integrated on DNA Substrates in Molecular Computing. Chembiochem 2024; 25:e202400080. [PMID: 38385968 DOI: 10.1002/cbic.202400080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
Due to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired crosstalk. In this minireview, we summarize recent developments in the integration of DNA logic gates into circuits localized on DNA substrates. This approach of all-DNA integrated circuits (DNA ICs) offers the advantages of biocompatibility, increased circuit response, increased circuit density, reduced unit concentration, facilitated circuit isolation, and facilitated cell uptake. DNA ICs can face similar challenges as their equivalent circuits operating in bulk solution (bulk circuits), and new physical challenges inherent in spatial localization. We discuss possible avenues to overcome these obstacles.
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Affiliation(s)
- Andrea C Bardales
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Viktor Smirnov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, 9 Lomonosova Str., St. Petersburg, Russian Federation
| | - Katherine Taylor
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
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3
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Ishaqat A, Zhang X, Liu Q, Zheng L, Herrmann A. Programming DNA Circuits for Controlled Immunostimulation through CpG Oligodeoxynucleotide Delivery. J Am Chem Soc 2023. [PMID: 37267596 DOI: 10.1021/jacs.2c09359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herein, we present a DNA circuit programmed for the delivery of CpG oligodeoxynucleotides (CpG ODNs) with the pharmacological immunostimulation function. The circuit employs a complementary DNA (cDNA) strand to deactivate the biological function of CpG ODNs via hybridization, while T7 exonuclease mediates the activation by hydrolyzing the cDNA and releasing the CpG ODN as an active moiety. We investigated the influence of several factors on the kinetic profile and temporal behavior of the circuit. These include the design of the cDNA strand, the concentration of the DNA duplex, and the concentration of T7 exonuclease. The DNA circuit's in vitro activation resulted in toll-like receptor 9 stimulation in the HEK-engineered cell line, as well as tumor necrosis factor-alpha release by J774A.1 macrophages. By programming the DNA circuit to control the release of the CpG ODN, we achieved an altered pharmacological profile with acute and potent immunostimulation, in comparison to a system without controlled CpG ODN release, which exhibited a slow and delayed response. Our findings demonstrate the potential of DNA circuits in controlling the pharmacological activity of DNA strands for controlled drug delivery.
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Affiliation(s)
- Aman Ishaqat
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Xiaofeng Zhang
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Qing Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, 25001 Wenzhou, China
| | - Lifei Zheng
- Wenzhou Institute, University of Chinese Academy of Sciences, 25001 Wenzhou, China
| | - Andreas Herrmann
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
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4
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Hu Y, Jia Y, Yang Y, Liu Y. Controllable DNA nanodevices regulated by logic gates for multi-stimulus recognition. RSC Adv 2023; 13:9003-9009. [PMID: 36950078 PMCID: PMC10025943 DOI: 10.1039/d3ra00295k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023] Open
Abstract
DNA biosensors have attracted considerable attention due to their great potential in environmental monitoring and medical diagnosis. Despite the great achievements, the single function and uncontrollability of the sensors restrict their further application. Therefore, it is necessary to construct controllable nanodevices with both sensing and responding capabilities to external stimuli. Herein, we develop a strategy to engineer structure-switching biosensors which can respond to external stimuli while preserving the sensing capability. The engineered nanodevice consists of an actuation module and a sensing module. Initially, the sensing module is disabled by a blocker strand which acts as an allosteric switch. Once the stimuli-responsive actuation module displaces the blocker DNA, the sensing module is activated. Based on the strategy, the engineered nanodevice could recognize both the target and external stimuli. As a demonstration of this strategy, a controllable Hg2+ sensor was designed, in which a 'YES', 'AND', and 'OR' logic gate is employed as the actuation module respectively to facilitate recognition of oligonucleotide inputs. The modular nature of the proposed strategy makes it easily generalizable to other structure-switching sensors. As a demonstration of this, we successfully apply it to the ATP sensor. The proposed strategy has potential in the fields of programmable biosensing, disease diagnosis, DNA computing, and intelligent nanodevices.
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Affiliation(s)
- Yingxin Hu
- School of Information Science and Technology, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
| | - Yufeng Jia
- School of Management, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
| | - Yuefei Yang
- School of Information Science and Technology, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
| | - Yanjun Liu
- School of Information Science and Technology, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
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5
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Song X, Yang C, Yuan R, Xiang Y. Electrochemical label-free biomolecular logic gates regulated by distinct inputs. Biosens Bioelectron 2022; 202:114000. [DOI: 10.1016/j.bios.2022.114000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/27/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
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6
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Li X, Yang H, He J, Yang B, Zhao Y, Wu P. Full liberation of 2-Aminopurine with nucleases digestion for highly sensitive biosensing. Biosens Bioelectron 2022; 196:113721. [PMID: 34673482 DOI: 10.1016/j.bios.2021.113721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/09/2021] [Accepted: 10/15/2021] [Indexed: 02/05/2023]
Abstract
2-Aminopurine (2-AP), a fluorescent isomer of adenine, is a popular fluorescent tag for DNA-based biosensors. The fluorescence of 2-AP is highly dependent on its microenvironment, i.e., almost non-fluorescent and merely fluorescent in dsDNA and ssDNA, respectively, but can be greatly brightened as mononucleotide. In most 2-AP-based biosensors, DNA transformation from dsDNA to ssDNA was employed, while selective digestion of 2-AP-labeled DNA with nucleases represents an appealing approach for improving the biosensor sensitivity. However, some detailed fundamental information, such as the reason for nuclease digestion, the influence of the labeling site, neighboring bases, or the label number of 2-AP for final signal output, are still largely unknown, which greatly limits the utility of 2-AP-based biosensors. In this work, using both steady- and excited-state fluorescence (lifetime), we demonstrated that nuclease digestion resulted in almost full liberation of 2-AP mononucleotides, and was free from labeling site and neighboring bases. Furthermore, we also found that nuclease digestion could lead to multiplexed sensitivity from increasing number of 2-AP labelling, but was not achievable for the conventional biosensors without full liberation of 2-AP. Considering the popularity of 2-AP in biosensing and other related applications, the above obtained information in sensitivity boosting is fundamentally important for future design of 2-AP-based biosensors.
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Affiliation(s)
- Xianming Li
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hang Yang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jialun He
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, China
| | - Bin Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peng Wu
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, China.
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7
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Chen D, Yang S, Han H, Song L, Huang D, Lin X, Xu X, Yang Q. The Construction of DNA Logic Gates Restricted to Certain Live Cells Based on the Structure Programmability and Aptamer-Cell Affinity of G-Quadruplexes. Chemistry 2021; 27:11627-11632. [PMID: 34046964 DOI: 10.1002/chem.202100913] [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: 03/12/2021] [Indexed: 11/09/2022]
Abstract
DNA computation is considered a fascinating alternative to silicon-based computers; it has evoked substantial attention and made rapid advances. Besides realizing versatile functions, implementing spatiotemporal control of logic operations, especially at the cellular level, is also of great significance to the development of DNA computation. However, developing simple and efficient methods to restrict DNA logic gates performing in live cells is still a challenge. In this work, a series of DNA logic gates was designed by taking full advantage of the diversity and programmability of the G-quadruplex (G4) structure. More importantly, by further using the high affinity and specific endocytosis of cells to aptamer G4, an INHIBIT logic gate has been realized whose operational site is precisely restricted to specific live cells. The design strategy might have great potential in the field of molecular computation and smart bio-applications.
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Affiliation(s)
- Die Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P.R. China
| | - Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P.R. China
| | - Huayi Han
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P.R. China
| | - Lingbo Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P.R. China
| | - Dan Huang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Xiao Lin
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Xiaoping Xu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P.R. China
| | - Qianfan Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
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8
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Li Y, Liu J. Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds. Analyst 2021; 145:6753-6768. [PMID: 32909556 DOI: 10.1039/d0an00886a] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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9
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Mei M, Mu L, Liang S, Wang Y, She G, Shi W. A general configurational strategy to quencher-free aptasensors. Biosens Bioelectron 2021; 178:113025. [PMID: 33529860 DOI: 10.1016/j.bios.2021.113025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022]
Abstract
The aptasensor, developed from the aptamer, has aroused wide concern in recent years owing to its high sensitivity and specificity. However, the quenching unit involved in the most of the aptasensors is indispensable to the fabrication of an aptasensor, which would undoubtedly increase the complexity of the device. In this study, a facile strategy was developed for construction of the quencher-free aptasensors, in which the quenching units can be omitted, and only an aptamer strand and a fluorophore are necessary. Distinguishable from the configuration of the traditional ones, the aptasensors developed in this work rationally employed the intrinsic quenching abilities of the analytes to directly regulate the fluorescence of the fluorophore. Furthermore, the aptamer strand as a discriminatory unit efficiently captured the corresponding analytes to around the fluorophores. As a result, the fluorescence of the aptasensor can be significantly sensitive to the analytes. The generality of the current design is evidenced by the successful fabrication of seven quencher-free aptasensors for Cu2+, Ag+, Hg2+, ATP and dopamine through 6-FAM labeling aptamers of Cu2+, Ag+, Hg2+, ATP, dopamine, 5-TAMRA and ROX labeling aptamers of Cu2+. Present strategy endows an aptasensor with a simple structure, high selectivity and fine sensitivity. The configuration of the quencher-free aptasensors fabricated in this work can be readily utilized for more aptasensors.
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Affiliation(s)
- Mingliang Mei
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixuan Mu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Sen Liang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangwei She
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wensheng Shi
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Jia Y, Hu Y. Cofactor-assisted three-way DNA junction-driven strand displacement. RSC Adv 2021; 11:30377-30382. [PMID: 35480263 PMCID: PMC9041134 DOI: 10.1039/d1ra05242j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
Toehold-mediated strand displacement is widely used to construct and operate DNA nanodevices. Cooperative regulation of strand displacement with diverse factors is pivotal in the design and construction of functional and dynamic devices. Herein, a cofactor-assisted three-way DNA junction-driven strand displacement strategy was reported, which could tune the reaction kinetics by the collaboration of DNA and other types of stimulus. This strategy is responsive to various inputs by incorporation of the specific sequence into the three-way junction structure. Specifically, the cooperation of multiple factors changes the conformation of the specific domain and promotes the reaction. To demonstrate the strategy, adenosine triphosphate (ATP), HG2+, and pH were used as cofactors to modulate the displacement reaction. The electrophoresis and fluorescence experiments showed that the cooperative regulation of the strand displacement reaction could be achieved by diverse factors using this strategy. The proposed strategy provides design flexibility for dynamic DNA devices and may have potential in biosensing and biocomputing. Cooperative regulation of strand displacement with diverse factors was achieved by a cofactor-assisted three-way DNA junction-driven strategy. Using this strategy nanodevices reacted to various inputs by incorporating a specific sequence into the three-way junction structure.![]()
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Affiliation(s)
- Yufeng Jia
- School of Economics and Management, Shijiazhuang Tiedao University, Shijiazhuang 050043, P. R. China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043, P. R. China
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11
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Fan D, Wang J, Wang E, Dong S. Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001766. [PMID: 33344121 PMCID: PMC7740092 DOI: 10.1002/advs.202001766] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Indexed: 05/11/2023]
Abstract
DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- Present address:
Institute of ChemistryThe Hebrew University of JerusalemJerusalem91904Israel
| | - Juan Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
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12
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Chen D, Wu Z, Xu X, Yang S. A Supramolecular Counter Circuit Based on Cyanine Dye Assembly. Chemistry 2020; 26:13235-13240. [PMID: 32337743 DOI: 10.1002/chem.202001240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/16/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Die Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology West China School of Pharmacy Sichuan University Chengdu 610041 P. R. China
| | - Zhiming Wu
- College of Computer Science Sichuan University Chengdu 610065 P. R. China
| | - Xiaoping Xu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology West China School of Pharmacy Sichuan University Chengdu 610041 P. R. China
| | - Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology West China School of Pharmacy Sichuan University Chengdu 610041 P. R. China
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13
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Tian Z, Peng P, Wang H, Zheng J, Shi L, Li T. Aptamer-Braked Multi-hairpin Cascade Circuits for Logic-Controlled Label-Free In Situ Bioimaging. Anal Chem 2020; 92:10357-10364. [PMID: 32600028 DOI: 10.1021/acs.analchem.0c00583] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As a common hairpin-based amplification strategy, catalytic-hairpin assembly (CHA) has been widely used to construct various DNA circuits for biosensing and imaging. However, the hairpin substrates can potentially react without catalysts and result in circuit leakage, which may be quite severe in a CHA reaction consisting of three or four hairpins due to the formation of stable three-/four-way junction product. To circumvent this problem, here we introduce a well-designed ATP aptamer as a DNA brake into a four-hairpin cascade circuit, where the triggering toehold is blocked by the aptamer brake and thus the circuit leakage decreases dramatically. Such an aptamer-braked DNA circuit is then employed to build an AND logic gate in response to multiple external stimuli in acidic cell membrane microenvironments. Induced by a bimolecular i-motif that binds thioflavin T (ThT), the dimerization of a four-way junction in situ assembled on the cell surface is accomplished, enabling the logic-controlled cell membrane imaging in a label-free manner. Our design would be applicable to other hairpin-based amplification strategies and may find more applications in the construction of multiresponsive DNA cascade circuits in complex living systems.
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Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Jiao Zheng
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
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14
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Abstract
In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.
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Affiliation(s)
- Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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15
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Wang H, Peng P, Wang Q, Du Y, Tian Z, Li T. Environment-Recognizing DNA-Computation Circuits for the Intracellular Transport of Molecular Payloads for mRNA Imaging. Angew Chem Int Ed Engl 2020; 59:6099-6107. [PMID: 31981393 DOI: 10.1002/anie.201916432] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/21/2020] [Indexed: 01/04/2023]
Abstract
Programming intelligent DNA nanocarriers for the targeted transport of molecular payloads in living cells has attracted extensive attention. In vivo activation of these nanocarriers usually relies on external light irradiation. An interest is emerging in the automatic recognition of intracellular surroundings by nanocarriers and their in situ activation under the control of programmed DNA-computation circuits. Herein, we report the integration of DNA circuits with framework nucleic acid (FNA) nanocarriers that consist of a truncated square pyramid (TSP) cage and a built-in duplex cargo containing an antisense strand of the target mRNA. An i-motif and ATP aptamer embedded in the TSP are employed as logic-controlling units to respond to H+ and ATP inside cellular compartments, triggering the release of the sensing element for fluorescent mRNA imaging. Logic-controlled FNA devices could be used to target drug delivery, enabling precise disease treatment.
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Affiliation(s)
- Huihui Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Yi Du
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Zhijin Tian
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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16
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Wang H, Peng P, Wang Q, Du Y, Tian Z, Li T. Environment‐Recognizing DNA‐Computation Circuits for the Intracellular Transport of Molecular Payloads for mRNA Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huihui Wang
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Pai Peng
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Qiwei Wang
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Yi Du
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Zhijin Tian
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Tao Li
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
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17
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Zheng J, Du Y, Wang H, Peng P, Shi L, Li T. Ultrastable Bimolecular G-Quadruplexes Programmed DNA Nanoassemblies for Reconfigurable Biomimetic DNAzymes. ACS NANO 2019; 13:11947-11954. [PMID: 31589020 DOI: 10.1021/acsnano.9b06029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The relatively low stability and polymorphism of bimolecular G-quadruplexes (bi-G4s) are big difficulties that are faced in employing them to guide DNA assembly, as they are usually subject to a transformation into more stable tetramolecular or G-wire structures favored by K+ or Mg2+. Although bi-G4s benefit by additional duplex handles, a challenge remains in tailoring their intrinsic properties to resolve the above difficulties. Toward this challenge, here we engineer several ultrastable bi-G4s via replacing their nucleotide loops with special mini-hairpins, which consist of a GAA loop and a short GC-paired stem. Such a structural alteration favors the formation of G:C:G:C tetrads in the head-to-head folding topologies of bi-G4s and improves their thermal stability, with an increase in the melting temperature by up to 25 °C. It dramatically reduces their structural conversion into G-wires, verified by atomic force microscopy. These features enable the utilization of two well-chosen bi-G4s to shape a DNA nanotriangle into the desired framework nucleic acid (FNA) architectures such as "bowknot" and "butterfly" that are reversibly switched by the bi-G4s. On this basis, we further build a reconfigurable DNAzyme device to mimic the activation of human telomerase that is modulated by the G4 dimerization. Our designed ultrastable bi-G4s will offer a promising tool for dynamically manipulating intracellular DNA nanoassemblies with endogenous K+ and exploring the relationship between dimerization and function in some physiological processes.
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Affiliation(s)
- Jiao Zheng
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Yi Du
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Huihui Wang
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Pai Peng
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Lili Shi
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Tao Li
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
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18
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Du Y, Peng P, Li T. DNA Logic Operations in Living Cells Utilizing Lysosome-Recognizing Framework Nucleic Acid Nanodevices for Subcellular Imaging. ACS NANO 2019; 13:5778-5784. [PMID: 30978283 DOI: 10.1021/acsnano.9b01324] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA logic nanodevices that in situ operate within living cells have attracted increasing interest and shown great promise for gene regulation and target recognition. A challenge remains how to control their activation inside specific cellular compartments. Toward this goal, here we report a lysosome-recognizing framework nucleic acid (FNA) nanodevice using an i-motif and an ATP-binding aptamer (ABA) incorporated into a DNA triangular prism (DTP) as the logic-controlling units. Once entering the lysosomal compartments, the FNA device responds to lysosomal pH and ATP via the folding of i-motif and ABA, which triggers a structural change of FNA and the release of a reporter structure for subcellular imaging. With endogenous proton and ATP as two inputs, an AND logic gate is built and in situ operated within living lysosomes by pH and ATP modulation with external drug stimuli. Given the abnormal levels of pH and ATP within some cancer cells or dysfunctional lysosomal cells, in this context our designed FNA logic device may find extended applications in controllable drug release and disease treatment.
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Affiliation(s)
- Yi Du
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Pai Peng
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Tao Li
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
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19
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Tang Z, Yin ZX, Sun X, Cui JZ, Yang J, Wang RS. Dynamically NAND gate system on DNA origami template. Comput Biol Med 2019; 109:112-120. [PMID: 31054386 DOI: 10.1016/j.compbiomed.2019.04.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/21/2019] [Accepted: 04/21/2019] [Indexed: 12/22/2022]
Abstract
Molecular logic gates play an important role in many fields and DNA-based logic gates are the basis of DNA computers. A dynamically NAND gate system on the DNA origami template is established in this paper. Naturally, the system is stable in solution without any reaction. Different logical values are mapped into different DNA input strands. When logical values are entered into the system, the corresponding DNA input strands undergo a directed hybridization chain reaction (HCR) at corresponding positions on the DNA origami template. The operation results are identified by disassembly between the nanogold particles (AuNPs) and DNA origami template. The nanogold particles remain on the DNA origami template, indicating that the result is true; The nanogold particles are dynamically separated from the DNA origami template, indicating that the result is false. The simulation of the system through Visual DSD shows that the reaction strictly followed the designed direction, and no error products are generated during the reaction. These simulation results show that the system has the advantages of feasibility, stability and intelligence.
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Affiliation(s)
- Zhen Tang
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Zhi-Xiang Yin
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China.
| | - Xia Sun
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Jian-Zhong Cui
- School of Electronic and Information Engineering, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Jing Yang
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Ri-Sheng Wang
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
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20
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Chen J, Yang S, Yang C, Li J, Huang D, Lin X, Guo C, Zhou Q, Yang Q, Tang Y. A Visibly Observable, Programmable Supramolecular Logic Platform and Its Application in Smart Thiols Sensing. Chemistry 2019; 25:5691-5697. [PMID: 30741458 DOI: 10.1002/chem.201900060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/31/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jianchi Chen
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Shu Yang
- West China School of PharmacySichuan University Chengdu 610041 Sichuan P.R. China
| | - Chunrong Yang
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Jicheng Li
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Dan Huang
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Xiao Lin
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Chen Guo
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Qiuju Zhou
- Analysis & Testing CenterXinyang Normal University Xinyang 464000 Henan P.R. China
| | - Qianfan Yang
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of ChemistryChinese Academy of Sciences Beijing 100190 P.R. China
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21
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Nanoparticle-based electrochemiluminescence cytosensors for single cell level detection. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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