1
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Sun X, Hua W, Liu X, Jin J, Zhang J, Tian J, Zheng B, Jiang W, Yao D, Liang H. Programming of Supercrystals Using Replicable DNA-Functionalized Colloids. Angew Chem Int Ed Engl 2024; 63:e202403492. [PMID: 38482742 DOI: 10.1002/anie.202403492] [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: 02/19/2024] [Indexed: 04/09/2024]
Abstract
The development of self-replicating systems is of great importance in research on the origin of life. As the most iconic molecules, nucleic acids have provided prominent examples of the fabrication of self-replicating artificial nanostructures. However, it is still challenging to construct sophisticated synthetic systems that can create large-scale or three-dimensionally ordered nanomaterials using self-replicating nanostructures. By integrating a template system containing DNA-functionalized colloidal seeds with a simplified DNA strand-displacement circuit programmed subsystem to produce DNA-functionalized colloidal copies, we developed a facile enthalpy-mediated strategy to control the replication and catalytic assembly of DNA-functionalized colloids in a time-dependent manner. The replication efficiency and crystal quality of the resulting superlattice structures can be effectively increased by regulating the molar ratio of the template to the copy colloids. By constructing binary systems from two types of gold nanoparticles (or proteins), superlattice structures with different crystal symmetries can be obtained through the replication and catalytic assembly processes. This programmable enthalpy-mediated approach was easily leveraged to achieve the phase transformation and catalytic amplification of colloidal crystals starting from different initial template crystals. This work offers a potential way to construct self-replicating artificial systems that exhibit complicated phase behaviors and can produce large-scale superlattice nanomaterials.
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Affiliation(s)
- Xiaoyun Sun
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wenqiang Hua
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Xiaoyu Liu
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jing Jin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jianing Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jie Tian
- Material Test and Analysis Lab, Engineering and Materials Science Experiment Center, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, China
| | - Wei Jiang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Dongbao Yao
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
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2
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Sun X, Yao D, Liang H. pH-Controlled Resettable Modular DNA Strand-Displacement Circuits. NANO LETTERS 2023; 23:11540-11547. [PMID: 38085915 DOI: 10.1021/acs.nanolett.3c03265] [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: 12/28/2023]
Abstract
Sophisticated dynamic molecular systems with diverse functions have been fabricated by using the fundamental tool of toehold-mediated strand displacement (TMSD) in the field of dynamic DNA nanotechnology. However, simple approaches to reset these TMSD-based dynamic systems are lacking due to the difficulty in creating kinetically favored pathways to implement the backward resetting reactions. Here, we develop a facile proton-driven strategy to achieve complete resetting of a modular DNA circuit by integrating a pH-responsive intermolecular CG-C+ triplex DNA and an i-motif DNA into the conventional DNA substrate. The pH-programmed strategy allows modular DNA components to specifically associate/dissociate to promote the forward/backward TMSD reactions, thereby enabling the modular DNA circuit to be repeatedly operated at a constant temperature without generating any DNA waste products. Leveraging this tractable approach, we further constructed two resettable DNA logic gates used for logical computation and two resettable catalytic DNA systems with good performance in signal transduction and amplification.
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Affiliation(s)
- Xiaoyun Sun
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dongbao Yao
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
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3
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Yang P, Zhou R, Hu J, Du L, Li F, Chen J, Hou X. Lanthanide Encoded Logically Gated Micromachine for Simultaneous Detection of Nucleic Acids and Proteins by Elemental Mass Spectrometry. Anal Chem 2022; 94:17746-17750. [PMID: 36480455 DOI: 10.1021/acs.analchem.2c04494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA-based logic computing potentially for analysis of biomarker inputs and generation of oligonucleotide signal outputs is of great interest to scientists in diverse areas. However, its practical use for sensing of multiple biomarkers is limited by the universality and robustness. Based on a proximity assay, a lanthanide encoded logically gated micromachine (LGM-Ln) was constructed in this work, which is capable of responding to multiplex inputs in biological matrices. Under the logic function controls triggered by inputs and a Boolean "AND" algorithm, it is followed by an amplified "ON" signal to indicate the analytes (inputs). In this logically gated sensing system, the whole computational process does not involve strand displacement in an intermolecular reaction, and a threshold-free design is employed to generate the 0 and 1 computation via intraparticle cleavage, which facilitates the computation units and makes the "computed values" more reliable. By simply altering the affinity ligands for inputs' biorecognition, LGM-Ln can also be extended to multi-inputs mode and produce the robust lanthanide encoded outputs in the whole human serum for sensing nucleic acids (with the detection limit of 10 pM) and proteins (with the detection limit of 20 pM). Compared with a logically gated micromachine encoded with fluorophores, the LGM-Ln has higher resolution and no spectral overlaps for multiple inputs, thus holding great promise in multiplex analyses and clinical diagnosis.
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Affiliation(s)
- Peng Yang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, China.,Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Hu
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Lijie Du
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Junbo Chen
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiandeng Hou
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China.,Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
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4
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Dimitrov E, Toncheva-Moncheva N, Bakardzhiev P, Forys A, Doumanov J, Mladenova K, Petrova S, Trzebicka B, Rangelov S. Nucleic acid-based supramolecular structures: vesicular spherical nucleic acids from a non-phospholipid nucleolipid. NANOSCALE ADVANCES 2022; 4:3793-3803. [PMID: 36133345 PMCID: PMC9470030 DOI: 10.1039/d2na00527a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Vesicular spherical nucleic acids are dynamic nucleic acid-based supramolecular structures that are held together via non-covalent bonds. They have promising applications as drug and nucleic acid delivery materials, diagnostic and imaging tools and platforms for development of various therapeutic schemes. In this contribution, we report on vesicular spherical nucleic acids, constructed from a non-phospholipid nucleolipid - an original hybrid biomacromolecule, composed of a hydrophobic residue, resembling that of the naturally occurring phospholipids, and a DNA oligonucleotide strand. The nucleolipid was synthesized by coupling of dibenzocyclooctyne-functionalized oligonucleotide and azidated 1,3-dihexadecyloxy-propane-2-ol via an azide-alkyne click reaction. In aqueous solution it spontaneously self-associated into nanosized supramolecular structures, identified as unilamellar vesicles composed of a self-closed interdigitated bilayer. Vesicular structures were also formed upon intercalation of the nucleolipid via its lipid-mimetic residue in the phospholipid bilayer membrane of liposomes prepared from readily available and FDA-approved lipids (1,2-dipalmitoyl-rac-glycero-3-phosphocholine and cholesterol). The vesicular structures are thoroughly investigated by light scattering (dynamic, static, and electrophoretic) and cryogenic TEM and the physical characteristics, in particular, number of strands per particle, grafting density, and conformation of the strands, were compared to those of reference spherical nucleic acids. Finally, the vesicular structures were shown to exhibit cellular internalization with no need of transfection agents and enhanced colloidal and nuclease stability.
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Affiliation(s)
- Erik Dimitrov
- Institute of Polymers, Bulgarian Academy of Sciences Akad. G. Bonchev St. 103A 1113 Sofia Bulgaria
| | | | - Pavel Bakardzhiev
- Institute of Polymers, Bulgarian Academy of Sciences Akad. G. Bonchev St. 103A 1113 Sofia Bulgaria
| | - Aleksander Forys
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences M. Curie-Sklodowskiej 34 Zabrze Poland
| | - Jordan Doumanov
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski Dragan Tsankov Blvd. 8 1164 Sofia Bulgaria
| | - Kirilka Mladenova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski Dragan Tsankov Blvd. 8 1164 Sofia Bulgaria
| | - Svetla Petrova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski Dragan Tsankov Blvd. 8 1164 Sofia Bulgaria
| | - Barbara Trzebicka
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences M. Curie-Sklodowskiej 34 Zabrze Poland
| | - Stanislav Rangelov
- Institute of Polymers, Bulgarian Academy of Sciences Akad. G. Bonchev St. 103A 1113 Sofia Bulgaria
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5
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Zheng B, Dong H, Zhu J, Zhang Q, Yang S, Yao D. A rational design of a cascaded DNA circuit for nanoparticle assembly and its application in the discrimination of single-base changes. J Mater Chem B 2022; 10:4561-4567. [PMID: 35621087 DOI: 10.1039/d2tb00155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the field of dynamic DNA nanotechnology, a designable DNA assembly circuit based on the toehold-mediated strand displacement reaction has demonstrated its ability to program the self-assembly of nanoparticles. However, the laborious work for the modification of nanoparticles with oligonucleotides, the long assembly time, and the circuit leakage prevent its further and scalable applications. To this end, cascaded circuits composed of two recycling circles are rationally designed in this study. Through the pre-initiation of the autonomous reaction, nanoparticles as sensing elements and no additionally exposed bases on the substrate hybridized with fuel strand, the real assembly time and signal leakage for diagnostic application can be effectively reduced and eliminated, thus offering a promising methodology for future point-of-care testing.
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Affiliation(s)
- Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Huaze Dong
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Jinmiao Zhu
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Qi Zhang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Shiwei Yang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Dongbao Yao
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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6
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Li C, Li Z, Han W, Yin X, Liu X, Xiao S, Liang H. How fluorescent labels affect the kinetics of the toehold-mediated DNA strand displacement reaction. Chem Commun (Camb) 2022; 58:5849-5852. [PMID: 35467686 DOI: 10.1039/d2cc01072k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
End modification of the toehold domain or near to it using fluorophore dyes or quenchers can significantly modulate the kinetics of the toehold-mediated strand displacement reaction (TMSDR) by almost two orders of magnitude. The labels at the end of the signal strand impede the TMSDR, while those at the end of the toehold domain of the substrate strand accelerate the TMSDR kinetics.
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Affiliation(s)
- Chengxu Li
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Zhigang Li
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Wenjie Han
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Xue Yin
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Xiaoyu Liu
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Shiyan Xiao
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Haojun Liang
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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7
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, 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
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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8
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Xue Y, Wang Y, Feng S, Yan M, Huang J, Yang X. Label-Free and Sensitive Electrochemical Biosensor for Amplification Detection of Target Nucleic Acids Based on Transduction Hairpins and Three-Leg DNAzyme Walkers. Anal Chem 2021; 93:8962-8970. [PMID: 34130449 DOI: 10.1021/acs.analchem.1c01522] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleic acids are regarded as reliable biomarkers for the early diagnosis of various diseases. By ingeniously combining a transduction hairpin (THP) with the toehold-mediated strand displacement reaction (TSDR) to form three-leg DNAzyme walkers, for the first time, we constructed a label-free and sensitive electrochemical sensing system for the amplification detection of target nucleic acids. With microRNA-155 (miR-155) as a model target, the feasibility of the biosensing strategy and the conformational states of DNA in the recognition process were studied in detail on the basis of electrochemical and dual polarization interferometry techniques. With the assistance of THP, miR-155 indirectly triggered the TSDR between three hairpins (H1, H2, and H3), then massive Mg2+-dependent three-leg DNAzyme walkers were formed in aqueous solutions. After the binding/cleaving/moving process of three-leg DNAzyme walkers on the electrode surface modified with substrate hairpins (SHPs), a number of single-stranded DNAs (ssDNAs) were generated. Hence, the interaction of methylene blue (MB) with the duplex section of SHPs was impeded, which brought about a decreased electrochemical signal. Benefiting from the cyclic amplification of the TSDR and the higher cleavage activity of three-leg DNAzyme walkers, the proposed sensing strategy showed remarkable improvement in sensitivity with a low detection limit of 0.27 fM for miR-155. Owing to the precise design of the THP, this method exhibited excellent specificity to distinguish miR-155 from the single-base and triplex-base mismatched sequences. This sensing strategy importing the flexible THP can be utilized to detect various nucleic acid biomarkers by only redesigning the THP without changing the main circuit or reporter constructs, showing the great versatility and potential for the early diagnostics and biological analysis.
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Affiliation(s)
- Yu Xue
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yu Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Sinuo Feng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Mengxia Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
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9
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Guo Y, Wei B, Zhou X, Yao D, Liang H. DNA Walker-Programmed Nanoparticle Superlattice. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a20090426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Liu C, Liu Y, Zhu E, Zhang Q, Wei X, Wang B. Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement. Nucleic Acids Res 2020; 48:10691-10701. [PMID: 33045746 PMCID: PMC7641751 DOI: 10.1093/nar/gkaa835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 01/19/2023] Open
Abstract
Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.
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Affiliation(s)
- Chanjuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Enqiang Zhu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
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11
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Ngamdee T, Yin LS, Vongpunsawad S, Poovorawan Y, Surareungchai W, Lertanantawong B. Target Induced-DNA strand displacement reaction using gold nanoparticle labeling for hepatitis E virus detection. Anal Chim Acta 2020; 1134:10-17. [PMID: 33059855 DOI: 10.1016/j.aca.2020.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022]
Abstract
DNA strand displacement is an attractive, enzyme-free target hybridization strategy for nano-biosensing. The target DNA induces a strand displacement reaction by replacing the pre-hybridized strand that is labeled with gold nanoparticles (AuNPs). Thus, the amount of displaced-AuNP-labeled strand is proportional to the amount of target DNA in the sample. The use of a magnetogenosensing technique to isolate the target DNA allows for a simple, one-pot detection approach, which minimizes possible carry-over contamination and pipetting errors. We sought a proof-of-concept for this technology in its ability to detect DNA-equivalent of hepatitis E virus (HEV), which causes acute viral hepatitis for which rapid and simple diagnostic methods remain limited. Signal detection was done via visual observation, spectrophotometry, and electrochemistry. The sensor demonstrated good sensitivity with detection limits of 10 pM (visual), 10 pM (spectrophotometry) and 1 fM (electrochemical). This sensor also exhibited high specificity for real target amplicons and could discriminate between perfect and mismatched sequences. Lyophilized biosensor reagents stored at 4 °C, 25 °C, and outdoor ambient temperature, were stable for up to 90, 50, and 40 days, respectively. The integration of magnetic separation and target DNA-induced strand displacement reaction in a dry reagent form makes the sensing platform easy-to-use and suitable for field settings.
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Affiliation(s)
- Tatchanun Ngamdee
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Lee Su Yin
- Faculty of Applied Sciences, AIMST University, Bedong, Kedah, 08100, Malaysia
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Werasak Surareungchai
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand; Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand
| | - Benchaporn Lertanantawong
- Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand; Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
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12
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Guo Y, Yao D, Zheng B, Sun X, Zhou X, Wei B, Xiao S, He M, Li C, Liang H. pH-Controlled Detachable DNA Circuitry and Its Application in Resettable Self-Assembly of Spherical Nucleic Acids. ACS NANO 2020; 14:8317-8327. [PMID: 32579339 DOI: 10.1021/acsnano.0c02329] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Toehold-mediated strand displacement reaction, the fundamental basis in dynamic DNA nanotechnology, has proven its extraordinary power in programming dynamic molecular systems. Programmed activation of the toehold in a DNA substrate is crucial for building sophisticated DNA devices with digital and dynamic behaviors. Here we developed a detachable DNA circuit by embedding a pH-controlled intermolecular triplex between the toehold and branch migration domain of the traditional "linear substrate". The reaction rate and the "on/off" state of the detachable circuit can be regulated by varying the pHs. Similarly, a two-input circuit composed of three pH-responsive DNA modules was then constructed. Most importantly, a resettable self-assembly system of spherical nucleic acids was built by utilizing the high detachability of the intermolecular triplex structure-based DNA circuit. This work demonstrated a dynamic DNA device that can be repeatedly operated at constant temperature without generating additional waste DNA products. Moreover, this strategy showed an example of recycling waste spherical nucleic acids from a self-assembly system of spherical nucleic acids. Our strategy will provide a facile approach for dynamic regulation of complex molecular systems and reprogrammable nanoparticle assembly structures.
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Affiliation(s)
- Yijun Guo
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, People's Republic of China
| | - Xianbao Sun
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Bing Wei
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Miao He
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Chengxu Li
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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13
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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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14
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Yao D, Bhadra S, Xiong E, Liang H, Ellington AD, Jung C. Dynamic Programming of a DNA Walker Controlled by Protons. ACS NANO 2020; 14:4007-4013. [PMID: 32167282 DOI: 10.1021/acsnano.9b08166] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have now constructed a four-legged DNA walker based on toehold exchange reactions whose movement is controlled by alternating pH changes. A well-characterized, pH-responsive CG-C+ triplex DNA was embedded into a tetrameric catalytic hairpin assembly (CHA) walker. The proton-controlled walker could autonomously move on otherwise unprogrammed microparticles surface, and the walking rate and steps of walking were efficiently controlled by pH. The starting and stopping of the walker, and its association and dissociation from the microparticles, could also be dynamically controlled by pH. The simple, programmable, and robust nature of this proton-controlled walker now provides the impetus for the development of a wide variety of more practical nanomachines.
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Affiliation(s)
- Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sanchita Bhadra
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Erhu Xiong
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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15
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Abstract
As a strategy for regulating entropy, thermal annealing is a commonly adopted approach for controlling dynamic pathways in colloid assembly. By coupling DNA strand-displacement circuits with DNA-functionalized colloid assembly, we developed an enthalpy-mediated strategy for achieving the same goal while working at a constant temperature. Using this tractable approach allows colloidal bonding to be programmed for synchronization with colloid assembly, thereby realizing the optimal programmability of DNA-functionalized colloids. We applied this strategy to conditionally activate colloid assembly and dynamically switch colloid identities by reconfiguring DNA molecular architectures, thereby achieving orderly structural transformations; leveraging the advantage of room-temperature assembly, we used this method to prepare a lattice of temperature-sensitive proteins and gold nanoparticles. This approach bridges two subfields: dynamic DNA nanotechnology and DNA-functionalized colloid programming.
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16
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Xing C, Chen Z, Dai J, Zhou J, Wang L, Zhang KL, Yin X, Lu C, Yang H. Light-Controlled, Toehold-Mediated Logic Circuit for Assembly of DNA Tiles. ACS APPLIED MATERIALS & INTERFACES 2020; 12:6336-6342. [PMID: 31918539 DOI: 10.1021/acsami.9b21778] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inspired by cytoskeletal structures that respond sensitively to environmental changes and chemical inputs, we report a strategy to trigger and finely control the assembly of stimulus-responsive DNA nanostructures with light under isothermal conditions. The strategy is achieved via integrating an upstream light-controlled, toehold-mediated DNA strand displacement circuit with a downstream DNA tile self-assembly process. By rationally designing an upstream DNA strand module, we further transform the upstream DNA strand displacement circuit to an "AND gate" circuit to control the assembly of DNA nanostructures. This example represents the demonstration of the spatial and temporal assembly of DNA nanostructures using a noninvasive chemical input. Such a light-controlled DNA logic circuit not only adds a new element to the tool box of DNA nanotechnology but also inspires us to assemble complex and responsive nanostructures.
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Affiliation(s)
- Chao Xing
- 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 350116 , P. R. China
- Fujian Provincial Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors , Minjiang University , Fuzhou 350108 , P. R. China
| | - Ziyi 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 350116 , P. R. China
| | - Junduan Dai
- 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 350116 , P. R. China
| | - Jie Zhou
- 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 350116 , P. R. China
| | - Liping Wang
- 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 350116 , P. R. China
| | - Kai-Long Zhang
- 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 350116 , P. R. China
| | - Xiaofei Yin
- First Institute of Oceanography, Ministry of Natural Resources , Qingdao 266061 , 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 350116 , 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 350116 , P. R. China
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17
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Applications of Spherical Nucleic Acid Nanoparticles as Delivery Systems. Trends Mol Med 2019; 25:1066-1079. [DOI: 10.1016/j.molmed.2019.08.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022]
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18
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Cui M, Zhou X, Chen X, Zheng W, Bian L, Li Z, Zheng B. Rapid and room temperature detection of single nucleotide variation with enhanced discrimination by crowding assisted allele specific extension. Chem Commun (Camb) 2019; 55:12052-12055. [PMID: 31535680 DOI: 10.1039/c9cc06229g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this paper we report the kinetics based detection of single nucleotide variation (SNV) at room temperature by allele specific extension with different concentrations and types of crowding agents. In general, the crowding conditions enhanced the specificity in the detection of SNV.
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Affiliation(s)
- Miao Cui
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China. and Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xiaoyu Zhou
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Xiaoyu Chen
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Weihao Zheng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Liming Bian
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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19
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Cascaded DNA circuits-programmed self-assembly of spherical nucleic acids for high signal amplification. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9603-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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A triple-amplification differential pulse voltammetry for sensitive detection of DNA based on exonuclease III, strand displacement reaction and terminal deoxynucleotidyl transferase. Biosens Bioelectron 2019; 143:111609. [DOI: 10.1016/j.bios.2019.111609] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/14/2019] [Accepted: 08/17/2019] [Indexed: 01/17/2023]
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21
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Li X, Sun X, Zhou J, Yao D, Xiao S, Zhou X, Wei B, Li C, Liang H. Enzyme-assisted waste-to-reactant transformation to engineer renewable DNA circuits. Chem Commun (Camb) 2019; 55:11615-11618. [PMID: 31501837 DOI: 10.1039/c9cc05941e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To date, implementation of renewable DNA circuits remains challenging due to issues including reactant depletion and waste accumulation. Herein we simultaneously addressed both issues through nicking enzyme-assisted waste-to-reactant transformation. As a proof-of-concept, a renewable entropy-driven catalytic DNA circuit was implemented, exhibiting a good renewability when replenishing fuel.
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Affiliation(s)
- Xiang Li
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Xianbao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, P. R. China.
| | - Junxiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Bing Wei
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Chengxu Li
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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22
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Wei B, Yao D, Zheng B, Zhou X, Guo Y, Li X, Li C, Xiao S, Liang H. Facile Strategy for Visible Disassembly of Spherical Nucleic Acids Programmed by Catalytic DNA Circuits. ACS APPLIED MATERIALS & INTERFACES 2019; 11:19724-19733. [PMID: 31083902 DOI: 10.1021/acsami.9b02107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The programmable toehold-mediated DNA-strand-displacement reaction has demonstrated its extraordinary capability in driving the spherical nucleic acid assembly. Here, a facile strategy of integrating a DNA-strand-displacement-based DNA circuit with a universal spherical nucleic acid aggregate system was developed for the visible disassembly of spherical nucleic acids. This integrated system exhibited rapid colorimetric response and good sensitivity in the disassembly reaction and demonstrated its capability in the application of single nucleotide polymorphism discrimination. Moreover, an OR logic gate used for multiplex detection was constructed through combining the fixed spherical nucleic acid disassembly system with two DNA circuits. This strategy will have great potential in the fabrication of a portable low-cost DNA diagnostic kit, and it is also a very promising method to be used in other applications, such as complex DNA networks and programmable phase transformation of nanoparticle superlattices.
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Affiliation(s)
- Bing Wei
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Dongbao Yao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering , Hefei Normal University , Hefei , Anhui 230061 , P. R. China
| | - Xiang Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Yijun Guo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Xiang Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Chengxu Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Shiyan Xiao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Haojun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
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23
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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24
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Li Y, Chen H, Dai Y, Chen T, Cao Y, Zhang J. Cellular interface supported toehold strand displacement cascade for amplified dual-electrochemical signal and its application for tumor cell analysis. Anal Chim Acta 2019; 1064:25-32. [PMID: 30982514 DOI: 10.1016/j.aca.2019.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 01/17/2023]
Abstract
In this work, toehold strand displacement cascade (TSDC) has been delicately designed and carried out on the cellular interface for the amplification and output of dual-electrochemical signal. Specifically, antibody cross-linked T strand can recognize cell which is linked with immune-magnetic bead. Subsequently, T strand on the cellular interface can mediate the occurrence of TSDC, resulting the change of SN3/S1-MB to SN3/S2-Fc ratio in the supernatant after magnetic separation. The resultant SN3/S1-MB and SN3/S2-Fc can be immobilized on the electrode interface through click chemistry and give the amplified double electrochemical signal. So the tumor cell amount can closely correlate with the change of the double signal. Except for output of the double signal for improvement of analytical accuracy, the double magnetic separation not only eliminate the interference of the complicated substances in serum, but also remove the influence of cell on click reaction on the electrode interface. So based on cellular interface supported TSDC for amplified dual-electrochemical signal, the established method has been successfully applied to analyze the tumor cells in serum accurately and sensitively.
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Affiliation(s)
- Yifei Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163, PR China
| | - Hong Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Yuhao Dai
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Tingjun Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
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25
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Zheng X, Yang J, Zhou C, Zhang C, Zhang Q, Wei X. Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis. Nucleic Acids Res 2019; 47:1097-1109. [PMID: 30541100 PMCID: PMC6379719 DOI: 10.1093/nar/gky1245] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/29/2022] Open
Abstract
Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers. However, those regulations required to change the sequences of whole DNAzyme, as separating parts and inserting extra DNA sequence. Inspired by the allosteric regulation of proteins in nature, a new allosteric strategy is proposed to regulate the activity of DNAzyme without DNA sequences changes. In this strategy, DNA strand displacement was used to regulate the DNAzyme structure, through which the activity of DNAzyme was well controlled. The strategy was applied to E6-type DNAzymes, and the operations of DNA logic circuit (YES, OR, AND, cascading and feedback) were established and simulated with the dynamic analyses. The allosteric regulation has potential to construct more complicated molecular systems, which can be applied to bio-sensing and detection.
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Affiliation(s)
- Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University, Shenyang 110136, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Changjun Zhou
- College of Mathematics and Computer sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Key laboratory of High Confidence Software Technologies, Ministry of Education, Beijing 100871, China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Scicence and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Scicence and Technology, Dalian University of Technology, Dalian 116024, China
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26
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Zhou X, Yao D, He M, Xiao S, Liang H. Optimizing the Toehold Strategy of On-Chip Nucleic Acid Hybridization Probe for the Discrimination of Single Nucleotide Polymorphism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14811-14816. [PMID: 30110553 DOI: 10.1021/acs.langmuir.8b02134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The synthetic DNA hybridization probe has proved its importance in biology and biotechnology. In this study, taking advantage of a novel analytical technique called dual polarization interferometry (DPI), the influence of the toehold strategy of on-chip DNA hybridization probe on the discrimination of single nucleotide polymorphism (SNP) was investigated. Through adjusting the toehold length, the toehold strategies of on-chip toehold exchange probe were thoroughly optimized. For the "6/5" probe, an optimal discrimination factor of 78% against the spurious target was achieved. Moreover, the ability of the on-chip probe in SNP discrimination was significantly enhanced compared to its pure solution counterpart. This simple and rapid detection method for SNP discrimination based on the on-chip toehold exchange probe will show great potential in disease diagnosis.
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Affiliation(s)
- Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Miao He
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
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27
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Li F, Gao Q, Yang M, Guo W. Regulation of Catalytic DNA Activities with Thermosensitive Gold Nanoparticle Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14932-14939. [PMID: 30277792 DOI: 10.1021/acs.langmuir.8b02149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The regulation of the activities of catalytic DNA is of great importance in many applications, especially in biosensing, controllable drug carriers, and gene therapy. In this work, the surfaces of gold nanoparticles (AuNPs) are simultaneously modified with a thermoresponsive polymer, poly( N-isopropylacrylamide) (pNIPAM), and catalytic DNA to form thermosensitive catalytic DNA/pNIPAM/AuNP systems. The thermosensitive pNIPAM on the surfaces of AuNPs enables the temperature-controlled catalytic activities of the system in a narrow temperature range. The catalytic DNA/pNIPAM/AuNP system exhibits almost no catalytic activity at temperatures below the lower critical solution temperature (LCST) of pNIPAM and become highly catalytic when the temperature is higher than the LCST. Two kinds of catalytic DNA, the entropy-driven DNA catalytic network and the Mg2+-dependent DNAzyme, were chosen as model catalytic systems, and the results showed that the regulation of catalytic activities for both systems was achieved efficiently. These systems may have important potentials in future biosensing and biomedical applications.
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Affiliation(s)
- Fengyun Li
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , P. R. China
| | - Qi Gao
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , P. R. China
| | - Mingjie Yang
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , P. R. China
| | - Weiwei Guo
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , 94 Weijin Road , Tianjin 300071 , P. R. China
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28
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Abstract
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic paradigms of DNA nanotechnology, we present a rationally designed synthetic platform that functions in an analogous manner to create complex DNA nanostructures. Starting from one type of DNA nanostructure, DNA strand displacement circuits were designed to interact and pass along the information encoded in the initial structure to mediate the self-assembly of a different type of structure, the final output structure depending on the type of circuit triggered. Using this concept of a DNA structure "trans-assembling" a different DNA structure through nonlocal strand displacement circuitry, four different schemes were implemented. Specifically, 1D ladder and 2D double-crossover (DX) lattices were designed to kinetically trigger DNA circuits to activate polymerization of either ring structures or another type of DX lattice under enzyme-free, isothermal conditions. In each scheme, the desired multilayer reaction pathway was activated, among multiple possible pathways, ultimately leading to the downstream self-assembly of the correct output structure.
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Affiliation(s)
- Jihoon Shin
- Hazards Monitoring Bionano Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon 34141 , Korea
| | - Junghoon Kim
- Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
| | - Sung Ha Park
- Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University , Suwon 16419 , Korea
| | - Tai Hwan Ha
- Hazards Monitoring Bionano Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon 34141 , Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology , Korea University of Science and Technology (UST) , Daejeon 34113 , Korea
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29
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Fern J, Schulman R. Modular DNA strand-displacement controllers for directing material expansion. Nat Commun 2018; 9:3766. [PMID: 30217991 PMCID: PMC6138645 DOI: 10.1038/s41467-018-06218-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/17/2018] [Indexed: 12/05/2022] Open
Abstract
Soft materials that swell or change shape in response to external stimuli show extensive promise in regenerative medicine, targeted therapeutics, and soft robotics. Generally, a stimulus for shape change must interact directly with the material, limiting the types of stimuli that may be used and necessitating high stimulus concentrations. Here, we show how DNA strand-displacement controllers within hydrogels can mediate size change by interpreting, amplifying, and integrating stimuli and releasing signals that direct the response. These controllers tune the time scale and degree of DNA-crosslinked hydrogel swelling and can actuate dramatic material size change in response to <100 nM of a specific biomolecular input. Controllers can also direct swelling in response to small molecules or perform logic. The integration of these stimuli-responsive materials with biomolecular circuits is a major step towards autonomous soft robotic systems in which sensing and actuation are implemented by biomolecular reaction networks. Materials which change shape in response to a trigger are of interest for soft robotics and targeted therapeutic delivery. Here, the authors report on the development of DNA-crosslinked hydrogels which can expand upon the detection of different biomolecular inputs mediated by DNA strand-displacement.
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Affiliation(s)
- Joshua Fern
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
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30
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Sun X, Wei B, Guo Y, Xiao S, Li X, Yao D, Yin X, Liu S, Liang H. A Scalable “Junction Substrate” to Engineer Robust DNA Circuits. J Am Chem Soc 2018; 140:9979-9985. [DOI: 10.1021/jacs.8b05203] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Xianbao Sun
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Yijun Guo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Shiyan Xiao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Xiang Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Dongbao Yao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Xue Yin
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Shiyong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
| | - Haojun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, People’s Republic of China
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31
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Cui M, Xiao X, Zhao M, Zheng B. Detection of single nucleotide polymorphism by measuring extension kinetics with T7 exonuclease mediated isothermal amplification. Analyst 2018; 143:116-122. [DOI: 10.1039/c7an00875a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Kinetics based detection of single nucleotide polymorphism at room temperature with high sensitivity and specificity.
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Affiliation(s)
- Miao Cui
- Department of Chemistry
- Centre of Novel Biomaterials
- The Chinese University of Hong Kong
- Shatin
- China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
| | - Bo Zheng
- Department of Chemistry
- Centre of Novel Biomaterials
- The Chinese University of Hong Kong
- Shatin
- China
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32
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Wang S, Lu S, Zhao J, Huang J, Yang X. Real-Time Study of the Interaction between G-Rich DNA Oligonucleotides and Lead Ion on DNA Tetrahedron-Functionalized Sensing Platform by Dual Polarization Interferometry. ACS APPLIED MATERIALS & INTERFACES 2017; 9:41568-41576. [PMID: 29099169 DOI: 10.1021/acsami.7b13477] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
G-quadruplex plays roles in numerous physiological and pathological processes of organisms. Due to the unique properties of G-quadruplex (e.g., forming G4/hemin complexes with catalytic activity and electron acceptability, binding with metal ions, proteins, fluorescent ligands, and so on), it has been widely applied in biosensing. But the formation process of G-quadruplex is not yet fully understood. Here, a DNA tetrahedron platform with higher reproducibility, regenerative ability, and time-saving building process was coupled with dual polarization interferometry technique for the real-time and label-free investigation of the specific interaction process of guanine-rich singled-stranded DNA (G-rich ssDNA) and Pb2+. The oriented immobilization of probes greatly decreased the spatial hindrance effect and improved the accessibility of the probes to the Pb2+ ions. Through real-time monitoring of the whole formation process of the G-quadruplex, we speculated that the probes on the tetrahedron platform initially stood on the sensing surface with a random coil conformation, then the G-rich ssDNA preliminarily formed unstable G-quartets by H-bonding and cation binding, subsequently forming a completely folded and stable quadruplex structure through relatively slow strand rearrangements. On the basis of these studies, we also developed a novel sensing platform for the specific and sensitive determination of Pb2+ and its chelating agent ethylenediaminetetraacetic acid. This study not only provides a proof-of-concept for conformational dynamics of G-quadruplex-related drugs and pathogenes, but also enriches the biosensor tools by combining nanomaterial with interfaces technique.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
- University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
- University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
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33
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Park Y, Lee CY, Park KS, Park HG. Enzyme-Free Colorimetric Detection of Cu2+by Utilizing Target-Triggered DNAzymes and Toehold-Mediated DNA Strand Displacement Events. Chemistry 2017; 23:17379-17383. [DOI: 10.1002/chem.201704346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Yeonkyung Park
- Department of Chemical and Biomolecular; Engineering (BK21+ Program); KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular; Engineering (BK21+ Program); KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering; Konkuk University; Seoul 05029 Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular; Engineering (BK21+ Program); KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
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34
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Wang X, Yan N, Song T, Wang B, Wei B, Lin L, Chen X, Tian H, Liang H. Robust Fuel Catalyzed DNA Molecular Machine for in Vivo MicroRNA Detection. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaojing Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Nan Yan
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Lin Lin
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Huayu Tian
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
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35
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Target-Triggered, Dual Amplification Strategy for Sensitive Electrochemical Detection of a Lymphoma-associated MicroRNA. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.03.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Abstract
Colloidal particles endowed with specific time-dependent interactions are a promising route for realizing artificial materials that have the properties of living ones. Previous work has demonstrated how this system can give rise to self-replication. Here, we introduce the process of colloidal catalysis, in which clusters of particles catalyze the creation of other clusters through templating reactions. Surprisingly, we find that simple templating rules generically lead to the production of huge numbers of clusters. The templating reactions among this sea of clusters give rise to an exponentially growing catalytic cycle, a specific realization of Dyson's notion of an exponentially growing metabolism. We demonstrate this behavior with a fixed set of interactions between particles chosen to allow a catalysis of a specific six-particle cluster from a specific seven-particle cluster, yet giving rise to the catalytic production of a sea of clusters of sizes between 2 and 11 particles. The fact that an exponentially growing cycle emerges naturally from such a simple scheme demonstrates that the emergence of exponentially growing metabolisms could be simpler than previously imagined.
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37
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SDR-ELISA: Ultrasensitive and high-throughput nucleic acid detection based on antibody-like DNA nanostructure. Biosens Bioelectron 2017; 90:481-486. [DOI: 10.1016/j.bios.2016.10.092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/13/2016] [Accepted: 10/31/2016] [Indexed: 12/11/2022]
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38
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Guo Y, Wei B, Xiao S, Yao D, Li H, Xu H, Song T, Li X, Liang H. Recent advances in molecular machines based on toehold-mediated strand displacement reaction. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Li L, Xiao X, Ge J, Han M, Zhou X, Wang L, Su X, Yu C. Discrimination Cascade Enabled Selective Detection of Single-Nucleotide Mutation. ACS Sens 2017; 2:419-425. [PMID: 28723215 DOI: 10.1021/acssensors.7b00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Owing to the significance of single nucleotide mutation (SNM) for personalized medicine, the detection of SNM with high accuracy has recently attracted considerable interest. Here, we present a kinetic method for selective detection of SNM based on a discrimination cascade constructed by combining the toehold strand displacement (TSD) and endonuclease IV (Endo IV) catalyzed hydrolysis. The single-nucleotide specificity of the two DNA reactions allows highly selective detection of all types of single nucleotide changes (including single-nucleotide insertion and deletion), achieving a high discrimination factor with a median of 491 which is comparable with recently reported methods. For the first time, the enzyme assisted nucleic acid assay was characterized by single molecule analysis on total internal reflection fluorescence microscope (TIRFM) suggesting that the two steps do not work independently and the rate of TSD can be tuned by Endo IV facilitated conformation selection. The effective discrimination of the point mutation of BRAF gene in cancer and normal cell line suggests that this method can be a prominent post-PCR genotyping assay.
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Affiliation(s)
- Lidan Li
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xianjin Xiao
- Family
Planning Research Institute/Center of Reproductive Medicine, Tongji
Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jingyang Ge
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Manli Han
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xu Zhou
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lei Wang
- 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
| | - Changyuan Yu
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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40
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Zhang Z, Fan TW, Hsing IM. Integrating DNA strand displacement circuitry to the nonlinear hybridization chain reaction. NANOSCALE 2017; 9:2748-2754. [PMID: 28155931 DOI: 10.1039/c6nr06589a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Programmable and modular attributes of DNA molecules allow one to develop versatile sensing platforms that can be operated isothermally and enzyme-free. In this work, we present an approach to integrate upstream DNA strand displacement circuits that can be turned on by a sequence-specific microRNA analyte with a downstream nonlinear hybridization chain reaction for a cascading hyperbranched nucleic acid assembly. This system provides a two-step amplification strategy for highly sensitive detection of the miRNA analyte, conducive for multiplexed detection. Multiple miRNA analytes were tested with our integrated circuitry using the same downstream signal amplification setting, showing the decoupling of nonlinear self-assembly with the analyte sequence. Compared with the reported methods, our signal amplification approach provides an additional control module for higher-order DNA self-assembly and could be developed into a promising platform for the detection of critical nucleic-acid based biomarkers.
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Affiliation(s)
- Zhuo Zhang
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Tsz Wing Fan
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - I-Ming Hsing
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong, China. and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
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41
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Fern J, Scalise D, Cangialosi A, Howie D, Potters L, Schulman R. DNA Strand-Displacement Timer Circuits. ACS Synth Biol 2017; 6:190-193. [PMID: 27744682 DOI: 10.1021/acssynbio.6b00170] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical circuits can coordinate elaborate sequences of events in cells and tissues, from the self-assembly of biological complexes to the sequence of embryonic development. However, autonomously directing the timing of events in synthetic systems using chemical signals remains challenging. Here we demonstrate that a simple synthetic DNA strand-displacement circuit can release target sequences of DNA into solution at a constant rate after a tunable delay that can range from hours to days. The rates of DNA release can be tuned to the order of 1-100 nM per day. Multiple timer circuits can release different DNA strands at different rates and times in the same solution. This circuit can thus facilitate precise coordination of chemical events in vitro without external stimulation.
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Affiliation(s)
- Joshua Fern
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dominic Scalise
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Angelo Cangialosi
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dylan Howie
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Leo Potters
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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42
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Hu S, Tang W, Zhao Y, Li N, Liu F. Ultra-specific discrimination of single-nucleotide mutations using sequestration-assisted molecular beacons. Chem Sci 2017; 8:1021-1026. [PMID: 28451240 PMCID: PMC5356502 DOI: 10.1039/c6sc03048c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/17/2016] [Indexed: 12/31/2022] Open
Abstract
Reliably distinguishing single-nucleotide mutations (SNMs) at low abundance is of great significance in clinical diagnosis. However, the specificity of most current SNM discrimination methods based on the Watson-Crick hybridization is seriously limited by the cross-reactivity of the probe with closely related unintended sequences. Herein, we propose a sequestration-assisted molecular beacon (MB) strategy for highly specific SNM discrimination. The new SNM discrimination system consists of a target-specific MB and a series of hairpin sequestering agents (SEQs). The rationally designed hairpin SEQs can effectively sequester the corresponding unintended sequences and thus dramatically improve the hybridization specificity of the MB in recognizing SNMs. The developed SNM discrimination method shows remarkably high specificity (discrimination factors ranging from 12 to 1144 with a median of 117) against 20 model SNMs, and can work rapidly and robustly over a wide range of conditions. Notably, our SNM discrimination method can be easily combined with PCR amplification for the detection of KRAS G12D (c.35G>A) and G12V (c.35G>T) mutations at abundance as low as 0.5%. This work expands the rule set of designing hybridization-based SNM discrimination strategies and shows promising potential application in clinical diagnosis.
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Affiliation(s)
- Shichao Hu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Wei Tang
- Institute of Materials , China Academy of Engineering Physics , Mianyang , 621700 , China
| | - Yan Zhao
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Na Li
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
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43
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Yao D, Xiao S, Zhou X, Li H, Wang B, Wei B, Liang H. Stacking modular DNA circuitry in cascading self-assembly of spherical nucleic acids. J Mater Chem B 2017; 5:6256-6265. [DOI: 10.1039/c7tb01307h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Integrated circuitries are successfully built through using the cascaded modular strategy with the assistance of stochastic simulations.
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Affiliation(s)
- Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Hui Li
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at the Microscale
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
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44
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Wang B, Zhou X, Yao D, Sun X, He M, Wang X, Yin X, Liang H. Contribution of gold nanoparticles to the catalytic DNA strand displacement in leakage reduction and signal amplification. Chem Commun (Camb) 2017; 53:10950-10953. [DOI: 10.1039/c7cc05832b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A new model using a gold nanoparticle (AuNP)–DNA system to constrain leakage and improve efficiency of catalytic toehold-mediated strand displacement reactions was outlined.
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Affiliation(s)
- Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Xianbao Sun
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Miao He
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Xiaojing Wang
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Xue Yin
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
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45
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Bi S, Yue S, Wu Q, Ye J. Triggered and catalyzed self-assembly of hyperbranched DNA structures for logic operations and homogeneous CRET biosensing of microRNA. Chem Commun (Camb) 2016; 52:5455-8. [PMID: 27010350 DOI: 10.1039/c6cc01308b] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Toehold-mediated strand displacement-based nanocircuits are developed by integrating catalytic hairpin assembly (CHA) with hybridization chain reaction (HCR), which achieves self-assembly of hyperbranched DNA structures and is readily utilized as an enzyme-free amplifier for homogeneous CRET detection of microRNA with high sensitivity and selectivity.
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Affiliation(s)
- Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University, Qingdao 266071, P. R. China.
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University, Qingdao 266071, P. R. China.
| | - Qiang Wu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Shandong Provincial Key Laboratory for Fishery Resources and Eco-environment, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, P. R. China
| | - Jiayan Ye
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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46
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Tanaka H, Zeravcic Z, Brenner MP. Mutation at Expanding Front of Self-Replicating Colloidal Clusters. PHYSICAL REVIEW LETTERS 2016; 117:238004. [PMID: 27982625 DOI: 10.1103/physrevlett.117.238004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 06/06/2023]
Abstract
We construct a scheme for self-replicating square clusters of particles in two spatial dimensions, and validate it with computer simulations in a finite-temperature heat bath. We find that the self-replication reactions propagate through the bath in the form of Fisher waves. Our model reflects existing colloidal systems, but is simple enough to allow simulation of many generations and thereby the first study of evolutionary dynamics in an artificial system. By introducing spatially localized mutations in the replication rules, we show that the mutated cluster population can survive and spread with the expanding front in circular sectors of the colony.
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Affiliation(s)
- Hidenori Tanaka
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Zorana Zeravcic
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Soft matter and chemistry laboratory, ESPCI PSL Research University, 75005 Paris, France
| | - Michael P Brenner
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
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47
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Oligonucleotide-based recognition in colloidal systems - opportunities and challenges. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Oishi M, Sugiyama S. An Efficient Particle-Based DNA Circuit System: Catalytic Disassembly of DNA/PEG-Modified Gold Nanoparticle-Magnetic Bead Composites for Colorimetric Detection of miRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5153-5158. [PMID: 27483209 DOI: 10.1002/smll.201601741] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/27/2016] [Indexed: 05/07/2023]
Abstract
An efficient particle-based DNA circuit system for a new colorimetric miRNA assay is designed and devised based on a catalytic disassembly strategy through a target miRNA-triggered DNA circuit mechanism. The new particle-based DNA circuit system shows a rapid color change as well as significant improvement of sensitivity without need for other enzymes or instruments.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan.
| | - Satomi Sugiyama
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan
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49
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Bi S, Yue S, Wu Q, Ye J. Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing. Biosens Bioelectron 2016; 83:281-6. [DOI: 10.1016/j.bios.2016.04.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/16/2016] [Accepted: 04/19/2016] [Indexed: 12/19/2022]
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50
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Isothermal RNA detection through the formation of DNA concatemers containing HRP-mimicking DNAzymes on the surface of gold nanoparticles. Biosens Bioelectron 2016; 80:67-73. [DOI: 10.1016/j.bios.2016.01.047] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/16/2016] [Accepted: 01/18/2016] [Indexed: 12/21/2022]
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