Computational investigation of Locked Nucleic Acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations

Poongavanam, Vasanthanathan, Madala, Praveen K., Højland, Torben and Veedu, Rakesh N. (2014) Computational investigation of Locked Nucleic Acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations. PLoS One, 9 7: 1-7. doi:10.1371/journal.pone.0102126


Author Poongavanam, Vasanthanathan
Madala, Praveen K.
Højland, Torben
Veedu, Rakesh N.
Title Computational investigation of Locked Nucleic Acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2014-07-18
Year available 2014
Sub-type Article (original research)
DOI 10.1371/journal.pone.0102126
Open Access Status DOI
Volume 9
Issue 7
Start page 1
End page 7
Total pages 7
Place of publication San Francisco, United States
Publisher Public Library of Science
Language eng
Abstract Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5′-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3′-endo conformation which in fact helps better orienting within the active site.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article # e102126

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
 
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Created: Fri, 25 Jul 2014, 19:22:16 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences