Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/13586
Title: Molecular dynamics simulation of ssDNA and cationic polythiophene
Authors: Nalıncı Bardak, Nehir
Kıbrıs, Erman
Demirci, Fethi Can
Elmacı Irmak, Nuran
Keywords: Polyelectrolyte
Cationic polythiophene
ssDNA
Molecular dynamics simulation
NAMD
MM-PBSA
Publisher: Elsevier
Abstract: In 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.
URI: https://doi.org/10.1016/j.jmgm.2023.108501
https://hdl.handle.net/11147/13586
ISSN: 1093-3263
1873-4243
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

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