Journal of Physical Chemistry B, volume 125, issue 33, pages 9499-9506
Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement
1
Université de Paris, ITODYS, CNRS, F-75006 Paris, France
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Publication type: Journal Article
Publication date: 2021-08-17
Journal:
Journal of Physical Chemistry B
Quartile SCImago
Q1
Quartile WOS
Q3
Impact factor: 3.3
ISSN: 15206106, 15205207
Materials Chemistry
Surfaces, Coatings and Films
Physical and Theoretical Chemistry
Abstract
Aptamers are a class of bioreceptors intensively used in current analytical tools dedicated to molecular diagnostics due to their ability to perform large structural reorganization upon target binding. However, there is a lack of methodologies allowing us to rationalize their structure in order to improve the transduction efficiency in aptamer sensors. We choose here, as a model system, a three-strand DNA structure as the probe, composed of two DNA strands anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to ampicillin (AMP). The DNA structure has been designed to show strong structural change upon AMP binding to its aptamer. Using a set of computational techniques including molecular dynamics simulations, we deeply investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses of ion distributions along the trajectories unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates the ability of computational investigations for the first time to drive, in silico, the design of aptasensors.
Top-30
Citations by journals
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Langmuir
1 publication, 20%
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Journal of Chemical Information and Modeling
1 publication, 20%
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ACS Applied Bio Materials
1 publication, 20%
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Russian Chemical Reviews
1 publication, 20%
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Frontiers in Bioengineering and Biotechnology
1 publication, 20%
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1
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Citations by publishers
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American Chemical Society (ACS)
3 publications, 60%
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Autonomous Non-profit Organization Editorial Board of the journal Uspekhi Khimii
1 publication, 20%
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Frontiers Media S.A.
1 publication, 20%
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- We do not take into account publications without a DOI.
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- Statistics recalculated weekly.
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Araujo Rocha M. et al. Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement // Journal of Physical Chemistry B. 2021. Vol. 125. No. 33. pp. 9499-9506.
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Araujo Rocha M., Piro B., Noel V., Barbault F. Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement // Journal of Physical Chemistry B. 2021. Vol. 125. No. 33. pp. 9499-9506.
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TY - JOUR
DO - 10.1021/acs.jpcb.1c05341
UR - https://doi.org/10.1021/acs.jpcb.1c05341
TI - Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement
T2 - Journal of Physical Chemistry B
AU - Araujo Rocha, Mario
AU - Noel, Vincent
AU - Barbault, Florent
AU - Piro, Benoit
PY - 2021
DA - 2021/08/17 00:00:00
PB - American Chemical Society (ACS)
SP - 9499-9506
IS - 33
VL - 125
SN - 1520-6106
SN - 1520-5207
ER -
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@article{2021_Araujo Rocha,
author = {Mario Araujo Rocha and Vincent Noel and Florent Barbault and Benoit Piro},
title = {Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement},
journal = {Journal of Physical Chemistry B},
year = {2021},
volume = {125},
publisher = {American Chemical Society (ACS)},
month = {aug},
url = {https://doi.org/10.1021/acs.jpcb.1c05341},
number = {33},
pages = {9499--9506},
doi = {10.1021/acs.jpcb.1c05341}
}
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Araujo Rocha, Mario, et al. “Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement.” Journal of Physical Chemistry B, vol. 125, no. 33, Aug. 2021, pp. 9499-9506. https://doi.org/10.1021/acs.jpcb.1c05341.