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Yao Y, Liu Y, Liu X, Zhang X, Shi P, Zhang X, Zhang Q, Wei X. Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios. iScience 2024; 27:109074. [PMID: 38361618 PMCID: PMC10867447 DOI: 10.1016/j.isci.2024.109074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
DNA tweezers, with their elegant simplicity and flexibility, have been pivotal in biosensing and DNA computing. However, conventional tweezers are confined to a binary transformation pre/post target signal recognition, limiting them to presence/absence judgments. This study introduces bubble DNA tweezers (BDT), capable of three distinct conformations based on variable target signal ratios. In contrast to traditional compact tweezers, BDT features a looser structure centered around a non-complementary bubble domain located between the tweezer arms' connecting axis and target signal recognition jaws. This bubble triggers toehold-free DNA strand displacement, leading to three conformational changes at different target signal concentrations. BDT detects presence/absence and true concentration with remarkable specificity and sensitivity. This adaptability is not confined to ideal scenarios, proving valuable in complex, noisy environments. Our method facilitates target DNA/miRNA signal quantification within a specific length range, promising applications in clinical research and environmental detection, while inspiring future biological assay innovations.
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Affiliation(s)
- Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
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2
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Liu Z, Rong G, Dong H, Zhang Y, Xu M, Baoxian Ye, Zhou Y. Ratiometric electrochemical biosensor based on lateral movement of multi-pedal DNA tetrahedron machine on biomimetic interface. Talanta 2024; 269:125454. [PMID: 38029606 DOI: 10.1016/j.talanta.2023.125454] [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: 06/20/2023] [Revised: 09/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
In this work, a lateral moving multi-pedal DNA tetrahedron machine (MTM) is designed and coupled with dual-signal output system to construct a biomimetic electrochemical ratiometric strategy for ultrasensitive target DNA analysis. The tetrahedral structure provided rigid support for the pedal, ensuring efficient replacement of the rail chain modified with ferrocene. By conjugating cholesterol molecules to one vertex of MTM, it is decorated on a lipid bilayer. This molecular architecture confers lateral movement of MTM on an electrode surface while prevents its detachment from the system. The methylene blue tagged hairpin probe provides constant power to support MTM swim on lipid bilayer. Compared with the conventional motion mode, the lateral moving mechanism has the fastest reaction rate and the highest signal-to-noise ratio. Additionally, the dual-signal reporting system further improves the accuracy of target detection on the basis of ensuring motion efficiency. The work improved movement efficiency and shortened time fragment. A linear relationship between the ratio value of two reporters and target DNA concentration was observed from 0.5 fM to 50 pM with a detection limit of 28 aM. The lateral motion mode of DNA machine coalescing with ratiometric system made this sensing platform ultrasensitive and accurate, which holds new avenue of early diagnosis.
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Affiliation(s)
- Zi Liu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China.
| | - Guoxiang Rong
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Hui Dong
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Yintang Zhang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Baoxian Ye
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yanli Zhou
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China.
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Zhao F, Frandsen M, Capodaglio S, Sleiman HF. DNA-Mediated Peptide Assembly into Protein Mimics. J Am Chem Soc 2024; 146:1946-1956. [PMID: 38226787 DOI: 10.1021/jacs.3c08984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.
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Affiliation(s)
- Fangzhou Zhao
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Martin Frandsen
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, Aarhus 8000, Denmark
| | - Sabrina Capodaglio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma I-43124, Italy
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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Zhao J, He C, Long Y, Lei J, Liu H, Hou J, Hou C, Huo D. 3D DNAzyme walker based electrochemical biosensor for attomolar level microRNA-155 detection. Anal Chim Acta 2023; 1276:341642. [PMID: 37573120 DOI: 10.1016/j.aca.2023.341642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
Herein, an ultrasensitive electrochemical biosensor for microRNA-155 (miR-155) detection based on the powerful catalytic and continuous walking signal amplification capability of 3D DNAzyme walker and the gold nanoparticles/graphene aerogels carbon fiber paper-based (AuNPs/GAs/CFP) flexible sensing electrode with excellent electrochemical performance was successfully constructed. In a proof-of-concept experiment, in the presence of miR-155, the DNAzyme strands anchored on the streptavidin-modified magnetic beads (MBs) silenced by locked strands can be activated, thus generating the walking arm of the 3D DNAzyme walker. Meanwhile, the substrate strands modified with Fe-MOF-NH2 nanoparticles were evenly distributed on the surface of MBs and served as tracks of the 3D DNAzyme walker. Once the DNAzyme strand was activated, the catalytic site in the substrate strand can be cleaved in the presence of Mn2+, and a large number of stumps modified with Fe-MOF-NH2 nanoparticles (output@Fe-MOF-NH2) will be generated during the continuous and efficient walking cleavage of the DNAzyme walker, driving the recognition-catalysis-release cycle process for signal amplification. Immediately afterwards, the signal was read out through the base complementary pairing of capture probe (PS) immobilized on the surface of the paper-based flexible sensing electrode AuNPs/GAs/CFP and signal probes output@Fe-MOF-NH2, thus achieving the quantitative detection of miR-155. Under optimal experimental conditions, the designed 3D DNAzyme walker-based biosensor exhibited a relatively lower limit of detection (LOD) of 56.23 aM, with a linear range of 100 aM to 100 nM. Overall, the proposed 3D DNAzyme walker biosensor exhibited good interference and reproducibility, demonstrating a promising future in the field of clinical disease diagnosis.
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Affiliation(s)
- Jiaying Zhao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Congjuan He
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Yanyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Jincan Lei
- Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, PR China
| | - Huan Liu
- Chongqing Institute for Food and Drug Control, Chongqing, 401121, PR China
| | - Jingzhou Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Postdoctoral Research Station, Chongqing University, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, PR China.
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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Zhang Y, Li JH, Zhang XL, Wang HJ, Yuan R, Chai YQ. Aluminum(III)-Based Organic Nanofibrous Gels as an Aggregation-Induced Electrochemiluminescence Emitter Combined with a Rigid Triplex DNA Walker as a Signal Magnifier for Ultrasensitive DNA Assay. Anal Chem 2023; 95:1686-1693. [PMID: 36541619 DOI: 10.1021/acs.analchem.2c04824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Due to effective tackling of the problems of aggregation-caused quenching of traditional ECL emitters, aggregation-induced electrochemiluminescence (AIECL) has emerged as a research hotspot in aqueous detection and sensing. However, the existing AIECL emitters still encounter the bottlenecks of low ECL efficiency, poor biocompatibility, and high cost. Herein, aluminum(III)-based organic nanofibrous gels (AOGs) are used as a novel AIECL emitter to construct a rapid and ultrasensitive sensing platform for the detection of Flu A virus biomarker DNA (fDNA) with the assistance of a high-speed and hyper-efficient signal magnifier, a rigid triplex DNA walker (T-DNA walker). The proposed AOGs with three-dimensional (3D) nanofiber morphology are assembled in one step within about 15 s by the ligand 2,2':6',2″-terpyridine-4'-carboxylic acid (TPY-COOH) and cheap metal ion Al3+, which demonstrates an efficient ECL response and outstanding biocompatibility. Impressively, on the basis of loop-mediated isothermal amplification-generated hydrogen ions (LAMP-H+), the target-induced pH-responsive rigid T-DNA walker overcomes the limitations of conventional single or duplex DNA walkers in walking trajectory and efficiency due to the entanglement and lodging of leg DNA, exhibiting high stability, controllability, and walking efficiency. Therefore, AOGs with excellent AIECL performance were combined with a CG-C+ T-DNA nanomachine with high walking efficiency and stability, and the proposed "on-off" ECL biosensor displayed a low detection limit down to 23 ag·μL-1 for target fDNA. Also, the strategy provided a useful platform for rapid and sensitive monitoring of biomolecules, considerably broadening its potential applications in luminescent molecular devices, clinical diagnosis, and sensing analysis.
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Affiliation(s)
- Yue Zhang
- Ministry of Education, College of Chemistry and Chemical Engineering, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Southwest University, Chongqing, Sichuan 400715, PR China
| | - Jia-Hang Li
- Ministry of Education, College of Chemistry and Chemical Engineering, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Southwest University, Chongqing, Sichuan 400715, PR China
| | - Xiao-Long Zhang
- Ministry of Education, College of Chemistry and Chemical Engineering, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Southwest University, Chongqing, Sichuan 400715, PR China
| | - Hai-Jun Wang
- Ministry of Education, College of Chemistry and Chemical Engineering, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Southwest University, Chongqing, Sichuan 400715, PR China
| | - Ruo Yuan
- Ministry of Education, College of Chemistry and Chemical Engineering, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Southwest University, Chongqing, Sichuan 400715, PR China
| | - Ya-Qin Chai
- Ministry of Education, College of Chemistry and Chemical Engineering, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Southwest University, Chongqing, Sichuan 400715, PR China
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