1
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Rosencrantz S, Matyash V, Rosencrantz RR, Fedorych O. A method to measure molecular hybridization. PLoS One 2024; 19:e0308084. [PMID: 39150912 PMCID: PMC11329138 DOI: 10.1371/journal.pone.0308084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/16/2024] [Indexed: 08/18/2024] Open
Abstract
Fluorescence-based oligonucleotide probes have a great importance in research of molecular interactions. Molecular beacons (MBs) are special case of fluorescent probes that form a stem-loop shape, bringing together a fluorophore and quencher, thus emitting fluorescence only when hybridized to a complementary target. Here we describe a new method for the quantitation of MB hybridization based on the measurement of changes in free energy instead of the fluorescence intensity. The MB energy state can be measured by micro-fluorescence detection. The approach allowed to determine hybridization energy of the MB with target nucleotide directly from fluorescence spectra and distinguish the MB in unfolded and hybridized states. Moreover, the method enabled us to discriminate between DNA duplexes with perfect complementarity or a single-nucleotide mismatch, based on the first direct experimental prove of enthalpy-entropy compensation.
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Affiliation(s)
- Sophia Rosencrantz
- Fraunhofer Institute for Applied Polymer Research IAP, Life Science and Bioprocesses, Potsdam, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Frankfurt am Main, Germany
| | | | - Ruben R Rosencrantz
- Fraunhofer Institute for Applied Polymer Research IAP, Life Science and Bioprocesses, Potsdam, Germany
- ICHORtec GmbH, Berlin, Germany
- Brandenburg University of Technology BTU, Institute for Materials Chemistry, Chair of Biofunctional Polymermaterials, Senftenberg, Germany
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2
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2024; 44:941-961. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
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Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
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3
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Wang X, Chen T, Ping Y, Dai Y, Yu P, Xie Y, Liu Z, Sun B, Duan X, Tao Z. Sequence-Guided Localization of DNA Hybridization Enables Highly Selective and Robust Genotyping. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307985. [PMID: 38084466 DOI: 10.1002/smll.202307985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/28/2023] [Indexed: 05/18/2024]
Abstract
Genetic variations are always related to human diseases or susceptibility to therapies. Nucleic acid probes that precisely distinguish closely related sequences become an indispensable requisite both in research and clinical applications. Here, a Sequence-guided DNA LOCalization for leaKless DNA detection (SeqLOCK) is introduced as a technique for DNA hybridization, where the intended targets carrying distinct "guiding sequences" act selectively on the probes. In silicon modeling, experimental results reveal considerable agreement (R2 = 0.9228) that SeqLOCK is capable of preserving high discrimination capacity at an extraordinarily wide range of target concentrations. Furthermore, SeqLOCK reveals high robustness to various solution conditions and can be directly adapted to nucleic acid amplification techniques (e.g., polymerase chain reaction) without the need for laborious pre-treatments. Benefiting from the low hybridization leakage of SeqLOCK, three distinct variations with a clinically relevant mutation frequency under the background of genomic DNA can be discriminated simultaneously. This work establishes a reliable nucleic acid hybridization strategy that offers great potential for constructing robust and programmable systems for molecular sensing and computing.
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Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Tao Chen
- Department of Blood Transfusion, Zhejiang Hospital, Hangzhou, 310052, China
| | - Ying Ping
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Yibei Dai
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Pan Yu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Yiyi Xie
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Zhenping Liu
- Department of Laboratory Medicine, Yuhang Branch of the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310058, China
| | - Bohao Sun
- Department of Pathology, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009, China
| | - Xiuzhi Duan
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Zhihua Tao
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
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4
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Mousivand M, Javan-Nikkhah M, Anfossi L, Di Nardo F, Salina M, Bagherzadeh K. High performance aptasensing platform development through in silico aptamer engineering for aflatoxin B1 monitoring. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2022]
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5
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Omran QQ, Fedorova O, Liu T, Pyle AM. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e74. [PMID: 35438748 PMCID: PMC9303364 DOI: 10.1093/nar/gkac242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Qusay Q Omran
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology Yale University, New Haven, CT 06520, USA
| | - Anna M Pyle
- To whom correspondence should be addressed. Tel: +1 203 432 5633; Fax: +1 203 432 5316;
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6
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Wong KL, Liu J. Factors and methods to modulate DNA hybridization kinetics. Biotechnol J 2021; 16:e2000338. [PMID: 34411451 DOI: 10.1002/biot.202000338] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.
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Affiliation(s)
- Kingsley L Wong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
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7
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Zhang Z, Liu N, Zhang Z, Xu D, Ma S, Wang X, Zhou T, Zhang G, Wang F. Construction of Aptamer-Based Molecular Beacons with Varied Blocked Structures and Targeted Detection of Thrombin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8738-8745. [PMID: 34270267 DOI: 10.1021/acs.langmuir.1c00994] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A kind of blocked aptamer-functionalized molecular beacon (MB) was designed as fluorescence sensors to detect thrombins by binding-induced "turn on" structural transformation. Three MBs named MB(8 + 8), MB(15 + 8), and MB(15 + 6) consisted of two single-stranded oligonucleotides. One long single-stranded oligonucleotide (abbreviated as SS) contained a thrombin aptamer sequence and was modified with a fluorescence group and quenching group on each end side. Another short single-stranded oligonucleotide (written as cDNA) was partially complementary to the long SS. It was interesting to find that the complementary sequence length of cDNA greatly influenced the structure of the MBs. The construction of MB experiments proved that MB(8 + 8) and MB(15 + 8) could form the quenching MBs but MB(15 + 6) could not. MB(8 + 8) was composed of a SS strand paired with a complementary cDNA(8 + 8), which was called one-to-one combination, while MB(15 + 8) was two-to-two combination and MB(15 + 6) was one-to-two combination. When the ratio of SS and cDNA (15 + 8) was 1:1, the quenching efficiency reached maximum. But with the molar ratio of SS and cDNA(8 + 8) increasing, the quenching efficiency increased continuously. Under the optimal conditions that we studied, the detection limit of thrombin by MB(8 + 8) and MB(15 + 8) was 0.19 and 1.2 nM, respectively. In addition, the assay proved to be selective, and the average recovery of thrombin detected by MB(8 + 8) and MB(15 + 8) in diluted serum was 95.4 and 94.5%, respectively.
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Affiliation(s)
- Zhiqing Zhang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Nana Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Zichen Zhang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Dongyan Xu
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Shuai Ma
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiufeng Wang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Ting Zhou
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Guodong Zhang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Wang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
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8
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Zhang L, Wang Y, Guo Y, Chen H, Yu W, Zhang Z, Xie G. A comprehensive system for detecting rare single nucleotide variants based on competitive DNA probe and duplex-specific nuclease. Anal Chim Acta 2021; 1166:338545. [PMID: 34023002 DOI: 10.1016/j.aca.2021.338545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Single nucleotide variants (SNVs) have emerged as increasingly important biomarkers, particularly in the diagnosis and prognosis of cancers. However, most SNVs are rarely detected in blood samples from cancer patients as they are surrounded by abundant concomitant wild-type nucleic acids. Herein, we design a system that features a combination of competitive DNA probe system (CDPS) and duplex-specific nuclease (DSN) that we referred to as CAD. A theoretical model was established for the CAD system based on reaction networks. Guided by the theoretical model, we found that a minor loss in sensitivity significantly improved the specificity of the system, thus creating a theoretical discrimination factor (DF) > 100 for most conditions. This non-equivalent tradeoff between sensitivity and specificity provides a new concept for the analysis of rare DNA-sequence variants. As a demonstration of practicality, we applied as-proposed CAD system to identify low variant allele frequency (VAF) in a synthetic template (0.1% VAF) and human genomic DNA (1% VAF). This work promises complete guidance for the design of enzyme-based nucleic acid analysis.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yufeng Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, 646000, PR China
| | - Huajian Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wen Yu
- Clinical Laboratory of Chongqing University Cancer Hospital, Chongqing, 400016, PR China
| | - Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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9
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Molecular diagnostic of toxigenic Corynebacterium diphtheriae strain by DNA sensor potentially suitable for electrochemical point-of-care diagnostic. Talanta 2021; 227:122161. [PMID: 33714465 DOI: 10.1016/j.talanta.2021.122161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022]
Abstract
The presented study is focused on the development of electrochemical genosensor for detection of tox gene fragment of toxigenic Corynebacterium diphtheriae strain. Together with our previous studies it fulfils the whole procedure for fast and accurate diagnostic of diphtheria at its early stage of infection with the use of electrochemical methods. The developed DNA sensor potentially can be used in more sophisticated portable device. After the electrochemical stem-loop probe structure optimization the conditions for real asymmetric PCR (aPCR) product detection were selected. As was shown it was crucial to optimize the magnesium and organic solvent concentrations in detection buffer. Under optimal conditions it was possible to selectively detect as low as 20.8 nM of complementary stand in 5 min or 0.5 nM in 30 min with sensitivity of 12.81 and 0.24 1⋅μM-1 respectively. The unspecific biosensor response was elucidated with the use of new electrode blocking agent, diethyldithiocarbamate. Its application in electrochemical genosensors lead to significant higher current values and the biosensor response even in conditions with magnesium ion depletion. The developed biosensor selectivity was examined using samples containing genetic material originated from a number of non-target bacterial species which potentially can be present in the human upper respiratory tract.
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10
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11
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Langford GJ, Raeburn J, Ferrier DC, Hands PJW, Shaver MP. Morpholino Oligonucleotide Cross-Linked Hydrogels as Portable Optical Oligonucleotide Biosensors. ACS Sens 2019; 4:185-191. [PMID: 30592402 DOI: 10.1021/acssensors.8b01208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Morpholino Oligonucleotides (MOs), an uncharged DNA analogue, are functionalized with an acrylamide moiety and incorporated into polymer hydrogels as responsive cross-links for microRNA sequence detection. The MO cross-links can be selectively cleaved by a short target analyte single-stranded DNA (ssDNA) sequence based on microRNA, inducing a distinct swelling response measured optically. The MO cross-links offer significant improvement over DNA based systems through improved thermal stability, no salt requirement and 1000-fold improved sensitivity over a comparative biosensor, facilitating a wider range of sensing conditions. Analysis was also achieved using a mobile phone camera, demonstrating portability.
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Affiliation(s)
- Geraint J. Langford
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, United Kingdom
| | - Jaclyn Raeburn
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, United Kingdom
| | - David C. Ferrier
- Institute for Integrated Micro and Nano Systems, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, United Kingdom
| | - Philip J. W. Hands
- Institute for Integrated Micro and Nano Systems, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, United Kingdom
| | - Michael P. Shaver
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, United Kingdom
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12
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Yan Y, Lu Y, Liu X, Zhang Y, Chen J. pH-Driven Precise Control of Hybridization Reaction Kinetics for Rapid DNA Assay. ChemistrySelect 2018. [DOI: 10.1002/slct.201801786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yishu Yan
- Department Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education; School of Pharmaceutical Sciences; Jiangnan University; 1800 Lihu Road Wuxi 214122 China
| | - Yuan Lu
- Key Lab of Industrial Biocatalysis; Ministry of Education; Department of Chemical Engineering; Tsinghua University Beijing; 100084 P.R.China
| | - Xiaoni Liu
- Department Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education; School of Pharmaceutical Sciences; Jiangnan University; 1800 Lihu Road Wuxi 214122 China
| | - Yan Zhang
- Department Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education; School of Pharmaceutical Sciences; Jiangnan University; 1800 Lihu Road Wuxi 214122 China
| | - Jinghua Chen
- Department Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education; School of Pharmaceutical Sciences; Jiangnan University; 1800 Lihu Road Wuxi 214122 China
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13
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Dunn KE, Trefzer MA, Johnson S, Tyrrell AM. Towards a Bioelectronic Computer: A Theoretical Study of a Multi-Layer Biomolecular Computing System That Can Process Electronic Inputs. Int J Mol Sci 2018; 19:E2620. [PMID: 30181468 PMCID: PMC6164260 DOI: 10.3390/ijms19092620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 01/06/2023] Open
Abstract
DNA molecular machines have great potential for use in computing systems. Since Adleman originally introduced the concept of DNA computing through his use of DNA strands to solve a Hamiltonian path problem, a range of DNA-based computing elements have been developed, including logic gates, neural networks, finite state machines (FSMs) and non-deterministic universal Turing machines. DNA molecular machines can be controlled using electrical signals and the state of DNA nanodevices can be measured using electrochemical means. However, to the best of our knowledge there has as yet been no demonstration of a fully integrated biomolecular computing system that has multiple levels of information processing capacity, can accept electronic inputs and is capable of independent operation. Here we address the question of how such a system could work. We present simulation results showing that such an integrated hybrid system could convert electrical impulses into biomolecular signals, perform logical operations and take a decision, storing its history. We also illustrate theoretically how the system might be able to control an autonomous robot navigating through a maze. Our results suggest that a system of the proposed type is technically possible but for practical applications significant advances would be required to increase its speed.
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Affiliation(s)
- Katherine E Dunn
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
| | - Martin A Trefzer
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
| | - Steven Johnson
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
| | - Andy M Tyrrell
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
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15
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Glasner H, Riml C, Micura R, Breuker K. Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry. Nucleic Acids Res 2017; 45:8014-8025. [PMID: 28549193 PMCID: PMC5570050 DOI: 10.1093/nar/gkx470] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/23/2017] [Indexed: 01/28/2023] Open
Abstract
Nucleobase methylations are ubiquitous posttranscriptional modifications of ribonucleic acids (RNA) that can substantially increase the structural diversity of RNA in a highly dynamic fashion with implications for gene expression and human disease. However, high throughput, deep sequencing does not generally provide information on posttranscriptional modifications (PTMs). A promising alternative approach for the characterization of PTMs, i.e. their identification, localization, and relative quantitation, is top-down mass spectrometry (MS). In this study, we have investigated how specific nucleobase methylations affect RNA ionization in electrospray ionization (ESI), and backbone cleavage in collisionally activated dissociation (CAD) and electron detachment dissociation (EDD). For this purpose, we have developed two new approaches for the characterization of RNA methylations in mixtures of either isomers of RNA or nonisomeric RNA forms. Fragment ions from dissociation experiments were analyzed to identify the modification type, to localize the modification sites, and to reveal the site-specific, relative extent of modification for each site.
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Affiliation(s)
- Heidelinde Glasner
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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16
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Xu L, Zhou W, Liu J. Enhanced DNA sensitized Tb 3+ luminescence in organic solvents for more sensitive detection. Anal Chim Acta 2017; 977:44-51. [PMID: 28577597 DOI: 10.1016/j.aca.2017.04.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/15/2017] [Accepted: 04/21/2017] [Indexed: 12/12/2022]
Abstract
DNA-sensitized Tb3+ luminescence spectroscopy is a powerful method for probing nucleic acids and developing biosensors. Its performance in organic solvents has yet to be explored. In this study, Tb3+ luminescence with nucleosides, nucleotides and DNA oligonucleotides in various organic solvents is studied. Tb3+ emission with single nucleotides is quenched up to 88% in dimethyl formamide (DMF), while its emission with nucleosides is enhanced. For the four 15-mer DNA homopolymers, the strongest absolute emission enhancement was achieved with C15. Similar emission properties are observed in other solvents including DMF, DMSO, acetonitrile methanol, ethanol, isopropanol and ethylene glycol. A few DNAzymes are tested as random DNA sequences all showing 1.4-6.9-fold emission enhancement in ethanol. A previously reported optimized sequence in water (G3T)5 is further enhanced by the solvents. Using this sequence, a detection limit of 5.5 nm Hg2+ is achieved in 25% ethanol solution. A similar Hg2+ sensitivity is also observed in a lake water mixed with ethanol. Luminescence lifetime is longer in DMF than in water. This study indicates that DNA-sensitized Tb3+ luminescence can be measured in water miscible solvents and most likely, with even stronger emission than that in water.
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Affiliation(s)
- Li Xu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan 528458, China; Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
| | - Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China; Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
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17
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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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18
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Gaß N, Gebhard J, Wagenknecht HA. Photocatalysis of a [2+2] Cycloaddition in Aqueous Solution Using DNA Three-Way Junctions as Chiral PhotoDNAzymes. CHEMPHOTOCHEM 2016. [DOI: 10.1002/cptc.201600034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Nadine Gaß
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Julian Gebhard
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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19
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Strand-Exchange Nucleic Acid Circuitry with Enhanced Thermo-and Structure- Buffering Abilities Turns Gene Diagnostics Ultra-Reliable and Environmental Compatible. Sci Rep 2016; 6:36605. [PMID: 27812041 PMCID: PMC5095676 DOI: 10.1038/srep36605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022] Open
Abstract
Catalytic hairpin assembly (CHA) is one of the most promising nucleic acid amplification circuits based on toehold-mediated strand exchange reactions. But its performance is usually ruined by fluctuated environmental temperatures or unexpected self-structures existing in most real-world targets. Here we present an amide-assistant mechanism that successfully reduces the prevalence of these problems for CHA and maximizes its thermo- and structure- buffering abilities. Such an organic amide-promoted CHA (shortened as OHT-CHA) can unprecedentedly amplify through 4 °C to 60 °C without rebuilding sequences or concerning target complexity. We are then for the first time able to employ it as a direct and universal signal booster for loop mediated isothermal reaction (LAMP). LAMP is one of the most promising point-of-care (POC) gene amplifiers, but has been hard to detect precisely due to structured products and haunted off-target amplicons. OHT-CHA guarantees a significant and reliable signal for LAMP reaction amplified from as little as 10−19 M virus gene. And one single set of OHT-CHA is qualified to any detection requirement, either in real-time at LAMP running temperature (~60 °C), or at end-point on a POC photon counter only holding environmental temperatures fluctuating between 4 °C to 42 °C.
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The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents. Biophys Rev 2016; 8:11-23. [PMID: 28510143 DOI: 10.1007/s12551-015-0188-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023] Open
Abstract
Organic solvents and apolar media are used in the studies of nucleic acids to modify the conformation and function of nucleic acids, to improve solubility of hydrophobic ligands, to construct molecular scaffolds for organic synthesis, and to study molecular crowding effects. Understanding how organic solvents affect nucleic acid interactions and identifying the factors that dominate solvent effects are important for the creation of oligonucleotide-based technologies. This review describes the structural and catalytic properties of DNA and RNA oligonucleotides in organic solutions and in aqueous solutions with organic cosolvents. There are several possible mechanisms underlying the effects of organic solvents on nucleic acid interactions. The reported results emphasize the significance of the osmotic pressure effect and the dielectric constant effect in addition to specific interactions with nucleic acid strands. This review will serve as a guide for the selection of solvent systems based on the purpose of the nucleic acid-based experiments.
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Ensslen P, Gärtner S, Glaser K, Colsmann A, Wagenknecht HA. A DNA-Fullerene Conjugate as a Template for Supramolecular Chromophore Assemblies: Towards DNA-Based Solar Cells. Angew Chem Int Ed Engl 2015; 55:1904-8. [DOI: 10.1002/anie.201509332] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/23/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Philipp Ensslen
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stefan Gärtner
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Konstantin Glaser
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Alexander Colsmann
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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22
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Ensslen P, Gärtner S, Glaser K, Colsmann A, Wagenknecht HA. Ein DNA-Fulleren-Konjugat als Templat für supramolekulare Chromophorstapel: Auf dem Weg zu DNA-basierten Solarzellen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Philipp Ensslen
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Stefan Gärtner
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Konstantin Glaser
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Alexander Colsmann
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Hans-Achim Wagenknecht
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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23
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Liu M, Wang Z, Pan L, Cui Y, Liu Y. A SERS/fluorescence dual-mode nanosensor based on the human telomeric G-quadruplex DNA: Application to mercury (II) detection. Biosens Bioelectron 2015; 69:142-7. [PMID: 25725462 DOI: 10.1016/j.bios.2015.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/24/2015] [Accepted: 02/06/2015] [Indexed: 11/17/2022]
Abstract
DNA-metal nanoparticle conjugates have been increasingly exploited for sensing purposes over the past decades. However, most of the existing strategies are operated with canonical DNA structures, such as single-stranded forms, stem-loop structures, and double helix structures. There is intense interest in the development of nano-system based on high order DNA secondary structures. Herein, we propose a SERS/fluorescence dual-mode nanosensor, where the signal transduction mechanism is based on the conformational switching of the human telomeric G-quadruplex DNA. The nanosensor exhibits excellent SERS/fluorescence responses to the complementary strands of G-quadruplexes. Based on T-Hg(2+)-T coordination chemistry, this sensor is effectively applied to determination of Hg(2+) in buffer solution and real samples. It achieves a limit of detection (LOD) as low as 1ppt, which is ~100 times more sensitive than conventional optical sensors. We anticipate that the proposed G-quadruplex-based nanosensor could be applied to the analysis of other metal ions and small molecules in environmental samples and biological systems.
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Affiliation(s)
- Min Liu
- College of Science, China Three Gorges University, Yichang 443002, Hubei, China; Advanced Photonics Center, Southeast University, 2# Sipai Lou, Nanjing 210096, Jiangsu, China.
| | - Zhuyuan Wang
- Advanced Photonics Center, Southeast University, 2# Sipai Lou, Nanjing 210096, Jiangsu, China
| | - Liqing Pan
- College of Science, China Three Gorges University, Yichang 443002, Hubei, China
| | - Yiping Cui
- Advanced Photonics Center, Southeast University, 2# Sipai Lou, Nanjing 210096, Jiangsu, China
| | - Yiman Liu
- College of Science, China Three Gorges University, Yichang 443002, Hubei, China.
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24
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Zhang T, Shang C, Duan R, Hakeem A, Zhang Z, Lou X, Xia F. Polar organic solvents accelerate the rate of DNA strand replacement reaction. Analyst 2015; 140:2023-8. [DOI: 10.1039/c4an02302a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acceleration of the reaction rate by polar organic solvents during both simple and complicated DNA strand replacement reactions is reported.
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Affiliation(s)
- Tianchi Zhang
- Key Laboratory for Large-Format Battery Materials and System
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Chunli Shang
- Key Laboratory for Large-Format Battery Materials and System
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Ruixue Duan
- Key Laboratory for Large-Format Battery Materials and System
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Abdul Hakeem
- Key Laboratory for Large-Format Battery Materials and System
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Zhenyu Zhang
- Key Laboratory for Large-Format Battery Materials and System
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Xiaoding Lou
- Key Laboratory for Large-Format Battery Materials and System
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Fan Xia
- Key Laboratory for Large-Format Battery Materials and System
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
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25
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Cheng H, Wu JX, Zheng H, Xu W, Zhou L, Too HP, Choi WK. DNA hybridization on silicon nanowire platform prepared by glancing angle deposition and metal assisted chemical etching process. RSC Adv 2015. [DOI: 10.1039/c5ra07117h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Porous nanowire surface provides high capacity for oligonucleotide hybridization.
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Affiliation(s)
- H. Cheng
- Advanced Materials for Micro- and Nano-Systems
- Singapore-MIT Alliance
- Singapore
| | - J. X. Wu
- NUS Graduate School for Integrative Sciences and Engineering
- National University of Singapore
- Singapore
| | - H. Zheng
- GLOBALFOUNDRIES Singapore Pte. Ltd
- Singapore
| | - W. Xu
- Department of Electrical and Computer Engineering
- National University of Singapore
- Singapore
| | | | - H. P. Too
- Department of Biochemistry
- National University of Singapore
- Singapore
- Bioprocessing Technology Institute
- Singapore
| | - W. K. Choi
- Advanced Materials for Micro- and Nano-Systems
- Singapore-MIT Alliance
- Singapore
- NUS Graduate School for Integrative Sciences and Engineering
- National University of Singapore
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26
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Ensslen P, Fritz Y, Wagenknecht HA. Mixed non-covalent assemblies of ethynyl nile red and ethynyl pyrene along oligonucleotide templates. Org Biomol Chem 2014; 13:487-92. [PMID: 25374296 DOI: 10.1039/c4ob01860e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ethynyl pyrene and ethynyl nile red as modifications at the 5-position of 2'-deoxyuridines self-assemble non-covalently and specifically along oligo-2'-deoxyadenosines as templates. Oligo-2'-deoxyadenosines of the lengths (dA)10-(dA)20 are able to retain nearly exactly as many ethynyl nile red units in solution as binding sites are available on these templates. In contrast, in the presence of oligo-2'-thymidines the ethynyl nile red moieties are similarly insoluble to those in the absence of any oligonucleotide and yield an aggregate. The mixed assemblies of both chromophores are highly ordered, show left-handed chirality and yield dual fluorescence. The strong excitonic coupling indicates assemblies with a high degree of order. These results show that DNA represents an important supramolecular scaffold for the templated, helical and non-covalent arrangement not only for one type of chromophore but also for mixtures of two different chromophores.
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Affiliation(s)
- Philipp Ensslen
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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27
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Zhang Z, Song J, Besenbacher F, Dong M, Gothelf KV. Self-Assembly of DNA Origami and Single-Stranded Tile Structures at Room Temperature. Angew Chem Int Ed Engl 2013; 52:9219-23. [DOI: 10.1002/anie.201303611] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 11/06/2022]
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28
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Zhang Z, Song J, Besenbacher F, Dong M, Gothelf KV. Self‐Assembly of DNA Origami and Single‐Stranded Tile Structures at Room Temperature. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303611] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Zhao Zhang
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark)
| | - Jie Song
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark)
- School of Physical Science and Technology, Lanzhou University, Lanzhou 730000 (P. R. China)
| | - Flemming Besenbacher
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark)
| | - Mingdong Dong
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark)
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark)
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29
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Seckute J, Yang J, Devaraj NK. Rapid oligonucleotide-templated fluorogenic tetrazine ligations. Nucleic Acids Res 2013; 41:e148. [PMID: 23775794 PMCID: PMC3753649 DOI: 10.1093/nar/gkt540] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Template driven chemical ligation of fluorogenic probes represents a powerful method for DNA and RNA detection and imaging. Unfortunately, previous techniques have been hampered by requiring chemistry with sluggish kinetics and background side reactions. We have developed fluorescent DNA probes containing quenched fluorophore-tetrazine and methyl-cyclopropene groups that rapidly react by bioorthogonal cycloaddition in the presence of complementary DNA or RNA templates. Ligation increases fluorescence with negligible background signal in the absence of hybridization template. Reaction kinetics depend heavily on template length and linker structure. Using this technique, we demonstrate rapid discrimination between single template mismatches both in buffer and cell media. Fluorogenic bioorthogonal ligations offer a promising route towards the fast and robust fluorescent detection of specific DNA or RNA sequences.
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Affiliation(s)
- Jolita Seckute
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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30
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Bercovici M, Han CM, Liao JC, Santiago JG. Rapid hybridization of nucleic acids using isotachophoresis. Proc Natl Acad Sci U S A 2012; 109:11127-32. [PMID: 22733732 PMCID: PMC3396536 DOI: 10.1073/pnas.1205004109] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants.
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Affiliation(s)
- Moran Bercovici
- Mechanical Engineering, Stanford University, 440 Escondido Mall, Stanford, CA 94305; and
- Department of Urology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305
| | - Crystal M. Han
- Mechanical Engineering, Stanford University, 440 Escondido Mall, Stanford, CA 94305; and
| | - Joseph C. Liao
- Department of Urology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305
| | - Juan G. Santiago
- Mechanical Engineering, Stanford University, 440 Escondido Mall, Stanford, CA 94305; and
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31
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Yahiatène I, Doose S, Huser T, Sauer M. Correlation-Matrix Analysis of Two-Color Coincidence Events in Single-Molecule Fluorescence Experiments. Anal Chem 2012; 84:2729-36. [DOI: 10.1021/ac2030283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Idir Yahiatène
- Applied Laser Physics and Laser
Spectroscopy, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Sören Doose
- Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland,
97074 Würzburg, Germany
| | - Thomas Huser
- Applied Laser Physics and Laser
Spectroscopy, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
- Center for Biophotonics Science & Technology, University of California, Davis, Sacramento, California 95817, United States
| | - Markus Sauer
- Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland,
97074 Würzburg, Germany
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32
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Zeng X, Zhang X, Yang W, Jia H, Li Y. Fluorescence detection of adenosine triphosphate through an aptamer-molecular beacon multiple probe. Anal Biochem 2012; 424:8-11. [PMID: 22369893 DOI: 10.1016/j.ab.2012.01.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/21/2012] [Accepted: 01/23/2012] [Indexed: 12/31/2022]
Abstract
An aptamer-molecular beacon (MB) multiple fluorescent probe for adenosine triphosphate (ATP) assay is proposed in this article. The ATP aptamer was used as a molecular recognition part, and an oligonucleotide (short strand, SS) partially complementary with the aptamer and an MB was used as the other part. In the presence of ATP, the aptamer bound with it, accompanied by the hybridization of MB and SS and the fluorescence recovering. Wherever there is only very weak fluorescence can be measured in the absence of ATP. Based on the relationship of recovering fluorescence and the concentration of ATP, a method for quantifying ATP has been developed. The fluorescence intensity was proportional to the concentration of ATP in the range of 10 to 500 nM with a detection limit of 0.1 nM. Moreover, this method was able to detect ATP with high selectivity in the presence of guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP). This method is proved to be simple with high sensitivity, selectivity, and specificity.
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Affiliation(s)
- Xiaodan Zeng
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, Beijing 100081, People's Republic of China
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33
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Zhang DY, Chen SX, Yin P. Optimizing the specificity of nucleic acid hybridization. Nat Chem 2012; 4:208-14. [PMID: 22354435 DOI: 10.1038/nchem.1246] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 12/02/2011] [Indexed: 01/06/2023]
Abstract
The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed 'toehold exchange' probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg(2+) to 47 mM Mg(2+), and with nucleic acid concentrations from 1 nM to 5 µM. Experiments with RNA also showed effective single-base change discrimination.
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Affiliation(s)
- David Yu Zhang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.
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34
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Menhaj AB, Smith BD, Liu J. Exploring the thermal stability of DNA-linked gold nanoparticles in ionic liquids and molecular solvents. Chem Sci 2012. [DOI: 10.1039/c2sc20565c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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35
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Asanuma H, Akahane M, Kondo N, Osawa T, Kato T, Kashida H. Quencher-free linear probe with multiple fluorophores on an acyclic scaffold. Chem Sci 2012. [DOI: 10.1039/c2sc20732j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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36
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Asanuma H, Osawa T, Kashida H, Fujii T, Liang X, Niwa K, Yoshida Y, Shimada N, Maruyama A. A polycation-chaperoned in-stem molecular beacon system. Chem Commun (Camb) 2012; 48:1760-2. [DOI: 10.1039/c2cc16812j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Bhatt N, Huang PJJ, Dave N, Liu J. Dissociation and degradation of thiol-modified DNA on gold nanoparticles in aqueous and organic solvents. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:6132-7. [PMID: 21513322 DOI: 10.1021/la200241d] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gold nanoparticles functionalized with thiol-modified DNA have been widely used in making various nanostructures, colorimetric biosensors, and drug delivery vehicles. Over the past 15 years, significant progress has been made to improve the stability of such functionalized nanoparticles. The stability of the gold-thiol bond in this system, however, has not been studied in a systematic manner. Most information on the gold-thiol bond was obtained from the study of self-assembled monolayers (SAMs). In this study, we employed two fluorophore-labeled and thiol-modified DNAs. The long-term stability of the thiol-gold bond as a function of time, salt, temperature, pH, and organic solvent has been studied. We found that the bond spontaneously dissociated under all tested conditions. The dissociation was favored at high salt, high pH, and high temperature, and little DNA degradation was observed in our system. Most organic solvents showed a moderate protection effect on the gold-thiol bond. The stability of the gold-thiol bond in the DNA system was also compared with that in SAMs. While there are many similarities, we also observed opposite trends for the salt and ethanol effect. This study suggests that the purified DNA-functionalized gold nanoparticles should be freshly prepared and used in a day or two. Long-term storage should be carried out at relatively low temperature in low salt and slightly acidic buffers.
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Affiliation(s)
- Nishi Bhatt
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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38
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Menacher F, Wagenknecht HA. Ratiometric molecular beacons based on the perylene bisimide as a dimeric internal DNA base substitution. Photochem Photobiol Sci 2011; 10:1275-8. [PMID: 21547330 DOI: 10.1039/c1pp05091e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular beacons with an excitonically interacting perylene bisimide base pair show the presence of the complementary olignucleotide sequence by both absorption and fluorescence changes.
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Affiliation(s)
- Florian Menacher
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany
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