Cargando…
Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations
Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer-Verlag
2006
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087579/ https://www.ncbi.nlm.nih.gov/pubmed/16450112 http://dx.doi.org/10.1007/s00894-005-0085-8 |
_version_ | 1783509358984822784 |
---|---|
author | Jin, Hongwei Zheng, Suxin Wang, Zhanli Luo, Cheng Shen, Jianhua Jiang, Hualiang Zhang, Liangren Zhang, Lihe |
author_facet | Jin, Hongwei Zheng, Suxin Wang, Zhanli Luo, Cheng Shen, Jianhua Jiang, Hualiang Zhang, Liangren Zhang, Lihe |
author_sort | Jin, Hongwei |
collection | PubMed |
description | Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent under periodic boundary conditions using the AMBER force field and the particle mesh Ewald method. The Watson–Crick hydrogen-bonding patterns of the duplexes studied remained intact throughout the simulation. For the modified duplexes, the changes observed in the inter-base pair parameters and backbone torsional angles were primarily localized at the isonucleoside-inserted area. All five structures studied remained in the B-form family. The decreased stacking abilities indicated by the large changes in inter-base pair parameters and the large changes in backbones made the modified duplexes show a minor thermal destabilization in comparison with native DNA. The MM_PBSA method for estimating binding free energies on two complementary strands was used. The results showed that the binding free energies of isonucleoside-incorporated DNA duplexes were lower than the native DNA duplex, which is in good agreement with experimental observations. [Image: see text] |
format | Online Article Text |
id | pubmed-7087579 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Springer-Verlag |
record_format | MEDLINE/PubMed |
spelling | pubmed-70875792020-03-23 Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations Jin, Hongwei Zheng, Suxin Wang, Zhanli Luo, Cheng Shen, Jianhua Jiang, Hualiang Zhang, Liangren Zhang, Lihe J Mol Model Original Paper Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent under periodic boundary conditions using the AMBER force field and the particle mesh Ewald method. The Watson–Crick hydrogen-bonding patterns of the duplexes studied remained intact throughout the simulation. For the modified duplexes, the changes observed in the inter-base pair parameters and backbone torsional angles were primarily localized at the isonucleoside-inserted area. All five structures studied remained in the B-form family. The decreased stacking abilities indicated by the large changes in inter-base pair parameters and the large changes in backbones made the modified duplexes show a minor thermal destabilization in comparison with native DNA. The MM_PBSA method for estimating binding free energies on two complementary strands was used. The results showed that the binding free energies of isonucleoside-incorporated DNA duplexes were lower than the native DNA duplex, which is in good agreement with experimental observations. [Image: see text] Springer-Verlag 2006-02-01 2006 /pmc/articles/PMC7087579/ /pubmed/16450112 http://dx.doi.org/10.1007/s00894-005-0085-8 Text en © Springer-Verlag 2006 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. |
spellingShingle | Original Paper Jin, Hongwei Zheng, Suxin Wang, Zhanli Luo, Cheng Shen, Jianhua Jiang, Hualiang Zhang, Liangren Zhang, Lihe Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations |
title | Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations |
title_full | Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations |
title_fullStr | Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations |
title_full_unstemmed | Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations |
title_short | Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations |
title_sort | structural insights into the effect of isonucleosides on b-dna duplexes using molecular-dynamics simulations |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087579/ https://www.ncbi.nlm.nih.gov/pubmed/16450112 http://dx.doi.org/10.1007/s00894-005-0085-8 |
work_keys_str_mv | AT jinhongwei structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations AT zhengsuxin structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations AT wangzhanli structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations AT luocheng structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations AT shenjianhua structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations AT jianghualiang structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations AT zhangliangren structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations AT zhanglihe structuralinsightsintotheeffectofisonucleosidesonbdnaduplexesusingmoleculardynamicssimulations |