Mapping DNA Conformations Using Single-Molecule Conductance Measurements
DNA is an attractive material for a range of applications in nanoscience and nanotechnology, and it has recently been demonstrated that the electronic properties of DNA are uniquely sensitive to its sequence and structure, opening new opportunities for the development of electronic DNA biosensors. I...
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Format: | Article |
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MDPI AG
2023-01-01
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Series: | Biomolecules |
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Online Access: | https://www.mdpi.com/2218-273X/13/1/129 |
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author | Mashari Alangari Busra Demir Caglanaz Akin Gultakti Ersin Emre Oren Joshua Hihath |
author_facet | Mashari Alangari Busra Demir Caglanaz Akin Gultakti Ersin Emre Oren Joshua Hihath |
author_sort | Mashari Alangari |
collection | DOAJ |
description | DNA is an attractive material for a range of applications in nanoscience and nanotechnology, and it has recently been demonstrated that the electronic properties of DNA are uniquely sensitive to its sequence and structure, opening new opportunities for the development of electronic DNA biosensors. In this report, we examine the origin of multiple conductance peaks that can occur during single-molecule break-junction (SMBJ)-based conductance measurements on DNA. We demonstrate that these peaks originate from the presence of multiple DNA conformations within the solutions, in particular, double-stranded B-form DNA (dsDNA) and G-quadruplex structures. Using a combination of circular dichroism (CD) spectroscopy, computational approaches, sequence and environmental controls, and single-molecule conductance measurements, we disentangle the conductance information and demonstrate that specific conductance values come from specific conformations of the DNA and that the occurrence of these peaks can be controlled by controlling the local environment. In addition, we demonstrate that conductance measurements are uniquely sensitive to identifying these conformations in solutions and that multiple configurations can be detected in solutions over an extremely large concentration range, opening new possibilities for examining low-probability DNA conformations in solutions. |
first_indexed | 2024-03-09T13:26:23Z |
format | Article |
id | doaj.art-8666a2469fd449aea29dc72c6dc22018 |
institution | Directory Open Access Journal |
issn | 2218-273X |
language | English |
last_indexed | 2024-03-09T13:26:23Z |
publishDate | 2023-01-01 |
publisher | MDPI AG |
record_format | Article |
series | Biomolecules |
spelling | doaj.art-8666a2469fd449aea29dc72c6dc220182023-11-30T21:23:11ZengMDPI AGBiomolecules2218-273X2023-01-0113112910.3390/biom13010129Mapping DNA Conformations Using Single-Molecule Conductance MeasurementsMashari Alangari0Busra Demir1Caglanaz Akin Gultakti2Ersin Emre Oren3Joshua Hihath4Department of Electrical Engineering, Engineering College, University of Ha’il, Ha’il 55476, Saudi ArabiaBionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, TurkeyBionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, TurkeyBionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, TurkeyElectrical and Computer Engineering Department, University of California Davis, Davis, CA 95616, USADNA is an attractive material for a range of applications in nanoscience and nanotechnology, and it has recently been demonstrated that the electronic properties of DNA are uniquely sensitive to its sequence and structure, opening new opportunities for the development of electronic DNA biosensors. In this report, we examine the origin of multiple conductance peaks that can occur during single-molecule break-junction (SMBJ)-based conductance measurements on DNA. We demonstrate that these peaks originate from the presence of multiple DNA conformations within the solutions, in particular, double-stranded B-form DNA (dsDNA) and G-quadruplex structures. Using a combination of circular dichroism (CD) spectroscopy, computational approaches, sequence and environmental controls, and single-molecule conductance measurements, we disentangle the conductance information and demonstrate that specific conductance values come from specific conformations of the DNA and that the occurrence of these peaks can be controlled by controlling the local environment. In addition, we demonstrate that conductance measurements are uniquely sensitive to identifying these conformations in solutions and that multiple configurations can be detected in solutions over an extremely large concentration range, opening new possibilities for examining low-probability DNA conformations in solutions.https://www.mdpi.com/2218-273X/13/1/129single-molecule electronicsmolecular electronicssingle-molecule break junctionDNAG-quadruplexes |
spellingShingle | Mashari Alangari Busra Demir Caglanaz Akin Gultakti Ersin Emre Oren Joshua Hihath Mapping DNA Conformations Using Single-Molecule Conductance Measurements Biomolecules single-molecule electronics molecular electronics single-molecule break junction DNA G-quadruplexes |
title | Mapping DNA Conformations Using Single-Molecule Conductance Measurements |
title_full | Mapping DNA Conformations Using Single-Molecule Conductance Measurements |
title_fullStr | Mapping DNA Conformations Using Single-Molecule Conductance Measurements |
title_full_unstemmed | Mapping DNA Conformations Using Single-Molecule Conductance Measurements |
title_short | Mapping DNA Conformations Using Single-Molecule Conductance Measurements |
title_sort | mapping dna conformations using single molecule conductance measurements |
topic | single-molecule electronics molecular electronics single-molecule break junction DNA G-quadruplexes |
url | https://www.mdpi.com/2218-273X/13/1/129 |
work_keys_str_mv | AT masharialangari mappingdnaconformationsusingsinglemoleculeconductancemeasurements AT busrademir mappingdnaconformationsusingsinglemoleculeconductancemeasurements AT caglanazakingultakti mappingdnaconformationsusingsinglemoleculeconductancemeasurements AT ersinemreoren mappingdnaconformationsusingsinglemoleculeconductancemeasurements AT joshuahihath mappingdnaconformationsusingsinglemoleculeconductancemeasurements |