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Kim HS, Huang SM, Yingling YG. Sequence dependent interaction of single stranded DNA with graphitic flakes: atomistic molecular dynamics simulations. ACTA ACUST UNITED AC 2016. [DOI: 10.1557/adv.2016.91] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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2
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Li NK, Kim HS, Nash JA, Lim M, Yingling YG. Progress in molecular modelling of DNA materials. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.913792] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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3
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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Zhang QD, March G, Noel V, Piro B, Reisberg S, Tran LD, Hai LV, Abadia E, Nielsen PE, Sola C, Pham MC. Label-free and reagentless electrochemical detection of PCR fragments using self-assembled quinone derivative monolayer: application to Mycobacterium tuberculosis. Biosens Bioelectron 2011; 32:163-8. [PMID: 22186165 DOI: 10.1016/j.bios.2011.11.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 09/29/2011] [Accepted: 11/30/2011] [Indexed: 11/17/2022]
Abstract
We report a signal-on, label-free and reagentless electrochemical DNA biosensor, based on a mixed self-assembled monolayer of thiolated hydroxynaphthoquinone and thiolated oligonucleotide. Electrochemical changes resulting from hybridization were evidenced with oligonucleotide targets (as models), as well as with polymerase chain reaction (PCR) products related to different lineages of Mycobacterium tuberculosis strains. With pure oligonucleotides, this system achieves high sensitivity (∼300 pM of DNA target, i.e. 30 fmol in a 100 μL sample) and excellent selectivity, allowing to detect a single mismatch on a sequence of 20 bases. With PCR products, current changes are specific to the bacterial strain from which the PCR fragment is produced. In addition, the sensor response is of the signal-on type, giving a positive signal change upon hybridization, and therefore does not suffer from false positive responses due to non-specific adsorption of DNA.
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Affiliation(s)
- Q D Zhang
- Interfaces, Traitement, Organisation et Dynamiques des Systèmes, UMR CNRS 7086, Université Paris Diderot, Sorbonne Paris Cité 15 rue Jean Antoine de Baïf, 75205 Paris Cedex 13, France
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Lu H, Qi S, Mack J, Li Z, Lei J, Kobayashi N, Shen Z. Facile Hg2+ detection in water using fluorescent self-assembled monolayers of a rhodamine-based turn-on chemodosimeter formed via a “click” reaction. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm11319d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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March G, Noël V, Piro B, Reisberg S, Pham MC. Nanometric layers for direct, signal-on, selective, and sensitive electrochemical detection of oligonucleotides hybridization. J Am Chem Soc 2009; 130:15752-3. [PMID: 18973298 DOI: 10.1021/ja8047255] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a signal-on, reagentless electrochemical DNA biosensor, based on an electroactive self-assembled naphthoquinone derivative (JUG(thio)) monolayer. This system achieves highly sensitive (approximately 300 pM) and selective signal-on detection. Before hybridization, the single strand can interact with JUG(thio) and slow down the redox reaction. When the complementary target is added, the formation of the double helix eliminates the single strand/JUG(thio) interactions and the JUG(thio) redox rate, and hence the current increase.
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Affiliation(s)
- Grégory March
- Interfaces, Traitement, Organisation et Dynamiques des Systèmes, Université Paris 7-Denis Diderot, UMR 7086, 15 rue Jean de Baif, 75205 Paris cedex 13, France
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Goujon F, Bonal C, Limoges B, Malfreyt P. Molecular Dynamics Description of Grafted Monolayers: Effect of the Surface Coverage. J Phys Chem B 2008; 112:14221-9. [DOI: 10.1021/jp8028825] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Goujon
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - C. Bonal
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - B. Limoges
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - P. Malfreyt
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
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Balland V, Hureau C, Cusano AM, Liu Y, Tron T, Limoges B. Oriented immobilization of a fully active monolayer of histidine-tagged recombinant laccase on modified gold electrodes. Chemistry 2008; 14:7186-92. [PMID: 18600817 DOI: 10.1002/chem.200800368] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The formation of a dense monolayer of histidine-tagged recombinant laccase on gold electrodes by using a short thiol-NTA linker is described, as well as a kinetic analysis of the process by cyclic voltammetry. From a detailed analysis of the catalytic reduction of dioxygen by laccase in the presence of a one-electron redox mediator it can be concluded that the immobilized enzyme remains as active as in homogeneous solution.
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Affiliation(s)
- Véronique Balland
- Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, Université Paris Diderot, 2 place Jussieu, Paris Cedex 05, France.
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Zhao W, Ali MM, Brook MA, Li Y. Rolling circle amplification: applications in nanotechnology and biodetection with functional nucleic acids. Angew Chem Int Ed Engl 2008; 47:6330-7. [PMID: 18680110 DOI: 10.1002/anie.200705982] [Citation(s) in RCA: 431] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rolling circle amplification (RCA) is an isothermal, enzymatic process mediated by certain DNA polymerases in which long single-stranded (ss) DNA molecules are synthesized on a short circular ssDNA template by using a single DNA primer. A method traditionally used for ultrasensitive DNA detection in areas of genomics and diagnostics, RCA has been used more recently to generate large-scale DNA templates for the creation of periodic nanoassemblies. Various RCA strategies have also been developed for the production of repetitive sequences of DNA aptamers and DNAzymes as detection platforms for small molecules and proteins. In this way, RCA is rapidly becoming a highly versatile DNA amplification tool with wide-ranging applications in genomics, proteomics, diagnosis, biosensing, drug discovery, and nanotechnology.
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Affiliation(s)
- Weian Zhao
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, ON, L8P 4M1, Canada
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Zhao W, Ali M, Brook M, Li Y. Rolling-Circle-Amplifikation: Anwendungen in der Nanotechnologie und in der Biodetektion mit funktionellen Nucleinsäuren. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705982] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Mir M, Alvarez M, Azzaroni O, Tiefenauer L, Knoll W. Molecular architectures for electrocatalytic amplification of oligonucleotide hybridization. Anal Chem 2008; 80:6554-9. [PMID: 18652492 DOI: 10.1021/ac800560t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we describe a new platform suitable for electrocatalytic amplification of oligonucleotide hybridization based on the use of supramolecular bioconjugates incorporating ferrocene-labeled streptavidin. Our goals were aimed at designing a biosensing platform which could support highly reproducible and stable electrocatalytic amplification with maximum efficiency. The use of nonlabeled streptavidin as an underlying layer promotes a major improvement on the characteristics of the amplified electrochemical signal. In addition, the electrocatalytic current can be easily amplified by tuning the concentration of electron donor species in solution. Because of the fact that the redox labels are bioconjugated to the DNA strands, increasing the ionic strength does not lead to the loss of redox labels. More importantly, increasing the concentration of donors only involves the magnification of the signal without implying the permeation of donors (thus reducing the efficient electrocatalysis). This approach represents a major improvement on the use of electrocatalytically amplified DNA-sensing platforms, thus overcoming any possible limitation in connection with the reproducibility and reliability of this well-established method.
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Affiliation(s)
- Mònica Mir
- Max-Planck-Institut fur Polymerforschung, Ackermannweg 10 (55128) Mainz, Germany
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Nayak A, Suresh KA. Discogen−DNA Complex Films at Air−Water and Air−Solid Interfaces. J Phys Chem B 2008; 112:2930-6. [DOI: 10.1021/jp710084q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Alpana Nayak
- Raman Research Institute, Sadashivanagar, Bangalore 560 080, India
| | - K. A. Suresh
- Raman Research Institute, Sadashivanagar, Bangalore 560 080, India
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Wang K, Goyer C, Anne A, Demaille C. Exploring the motional dynamics of end-grafted DNA oligonucleotides by in situ electrochemical atomic force microscopy. J Phys Chem B 2007; 111:6051-8. [PMID: 17487999 DOI: 10.1021/jp070432x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce herein the use of atomic-force electrochemical microscopy (AFM-SECM) to simultaneously probe locally the conformation and motional dynamics of nanometer-sized single-stranded (ss) and double-stranded (ds) DNA oligonucleotides end-tethered to electrode surfaces. The ss-DNA system studied here consists of a low-density monolayer of (dT)20 oligonucleotides, 5'-thiol end-tethered onto a flat gold surface via a C6 alkyl linker and bearing at their free 3'-end a redox ferrocene label. It is shown that, as a result of the flexibility of the relatively long C6 linker, hinge motion, rather than elastic deformation of the DNA chain, is the major component of the dynamics of both the (dT)20 strand and its post-hybridized (dT-dA)20 duplex. DNA chain elasticity is nevertheless sufficiently contributing to the overall dynamics to result in approximately 4 times slower dynamics for (dT-dA)20 than for (dT)20. Taking advantage of this dissimilar dynamical behavior of ss- and ds-DNA, it is demonstrated that hybridization can be easily locally detected at the scale of approximately 200 molecules by AFM-SECM.
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Affiliation(s)
- Kang Wang
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université-CNRS No. 7591, Université de Paris 7--Denis Diderot, Paris Cedex 05, France
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Abstract
Electrochemical DNA biosensors exploit the affinity of single-stranded DNA for complementary strands of DNA and are used in the detection of specific sequences of DNA with a view towards developing portable analytical devices. Great progress has been made in this field but there are still numerous challenges to overcome. This review for researchers new to the field describes the components of electrochemical DNA biosensors and the important issues in their design. Methods of transducing DNA binding events are discussed along with future directions for DNA biosensors.
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Anne A, Bonnaudat C, Demaille C, Wang K. Enzymatic redox 3'-end-labeling of DNA oligonucleotide monolayers on gold surfaces using terminal deoxynucleotidyl transferase (TdT)-mediated single base extension. J Am Chem Soc 2007; 129:2734-5. [PMID: 17302416 DOI: 10.1021/ja067954v] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Agnès Anne
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université-CNRS No 7591 Université de Paris 7-Denis Diderot, 2 place Jussieu, 75251 Paris cedex 05, France.
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