Unraveling Bacterial Single-Stranded Sequence Specificities: Insights from Molecular Dynamics and MMPBSA Analysis of Oligonucleotide Probes.
Binding free energy
Electrostatics
Enterobacteriaceae
MMPBSA
Molecular dynamics
Oligonucleotide probe
Pasteurellaceae
Specificity
Vibrionaceae
Journal
Molecular biotechnology
ISSN: 1559-0305
Titre abrégé: Mol Biotechnol
Pays: Switzerland
ID NLM: 9423533
Informations de publication
Date de publication:
19 Feb 2024
19 Feb 2024
Historique:
received:
03
10
2022
accepted:
10
01
2024
medline:
20
2
2024
pubmed:
20
2
2024
entrez:
20
2
2024
Statut:
aheadofprint
Résumé
We utilized molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) free energy calculations to investigate the specificity of two oligonucleotide probes, namely probe B and probe D, in detecting single-stranded DNA (ssDNA) within three bacteria families: Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. Due to the limited understanding of molecular mechanisms in the previous research, we have extended the discussion to focus specifically on investigating the binding process of bacteria-probe DNA duplexes, with an emphasis on analyzing the binding free energy. The role of electrostatic contributions in the specificity between the oligonucleotide probes and the bacterial ssDNAs was investigated and found to be crucial. Our calculations yielded results that were highly consistent with the experimental data. Through our study, we have successfully exhibited the benefits of utilizing in-silico approaches as a powerful virtual-screening tool, particularly in research areas that demand a thorough comprehension of molecular interactions.
Identifiants
pubmed: 38374320
doi: 10.1007/s12033-024-01082-0
pii: 10.1007/s12033-024-01082-0
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Thailand Science Research and Innovation
ID : MRG6280217
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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