Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/13586
Full metadata record
DC FieldValueLanguage
dc.contributor.authorNalıncı Bardak, Nehir-
dc.contributor.authorKıbrıs, Erman-
dc.contributor.authorDemirci, Fethi Can-
dc.contributor.authorElmacı Irmak, Nuran-
dc.date.accessioned2023-07-27T19:49:55Z-
dc.date.available2023-07-27T19:49:55Z-
dc.date.issued2023-
dc.identifier.issn1093-3263-
dc.identifier.issn1873-4243-
dc.identifier.urihttps://doi.org/10.1016/j.jmgm.2023.108501-
dc.identifier.urihttps://hdl.handle.net/11147/13586-
dc.description.abstractIn this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak pi -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.en_US
dc.description.sponsorshipThis work was supported by the Scientific and Technological Research Council of Turkey, TUBITAK, under project numbers 119Z100. The numerical calculations reported in this paper were entirely performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources) . Computing resources used in this work were provided by the National Center for High Performance Computing of Turkey (UHeM) under grant number #1014132022#. We want to thank to Omit Hakan Yildiz for the inspiration for this study.en_US
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.relation.ispartofJournal of Molecular Graphics & Modellingen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectPolyelectrolyteen_US
dc.subjectCationic polythiopheneen_US
dc.subjectssDNAen_US
dc.subjectMolecular dynamics simulationen_US
dc.subjectNAMDen_US
dc.subjectMM-PBSAen_US
dc.titleMolecular dynamics simulation of ssDNA and cationic polythiopheneen_US
dc.typeArticleen_US
dc.departmentİzmir Institute of Technology. Chemistryen_US
dc.identifier.volume123en_US
dc.identifier.wosWOS:000999128600001en_US
dc.identifier.scopus2-s2.0-85157977278en_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıtr
dc.identifier.doi10.1016/j.jmgm.2023.108501-
dc.identifier.pmid37182506en_US
dc.authorscopusid58235479400-
dc.authorscopusid57221378339-
dc.authorscopusid58235260400-
dc.authorscopusid58235260500-
dc.identifier.scopusqualityQ2-
item.languageiso639-1en-
item.fulltextWith Fulltext-
item.grantfulltextembargo_20250101-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
item.openairetypeArticle-
crisitem.author.dept04.01. Department of Chemistry-
Appears in Collections:Chemistry / Kimya
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Files in This Item:
File SizeFormat 
1-s2.0-S1093326323000992-main.pdf
  Until 2025-01-01
3.53 MBAdobe PDFView/Open    Request a copy
Show simple item record



CORE Recommender

Page view(s)

76
checked on Jul 15, 2024

Google ScholarTM

Check




Altmetric


Items in GCRIS Repository are protected by copyright, with all rights reserved, unless otherwise indicated.