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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Main Authors: Mashari Alangari, Busra Demir, Caglanaz Akin Gultakti, Ersin Emre Oren, Joshua Hihath
Format: Article
Language:English
Published: MDPI AG 2023-01-01
Series:Biomolecules
Subjects:
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.
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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