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

F. Salsbury; V. Poongavanam; P.K. Madala; T. Højland; R.N. Veedu

doi:10.1371/journal.pone.0102126

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

Journal article

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Peer reviewed

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

F. Salsbury, V. Poongavanam, P.K. Madala, T. Højland and R.N. Veedu

PLoS ONE, Vol.9(7), e102126

2014

DOI: https://doi.org/10.1371/journal.pone.0102126

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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.

Details

Title: Computational investigation of Locked Nucleic Acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations
Authors/Creators: F. Salsbury (Author/Creator)
V. Poongavanam (Author/Creator) - University of Southern Denmark
P.K. Madala (Author/Creator) - The University of Queensland
T. Højland (Author/Creator) - University of Southern Denmark
R.N. Veedu (Author/Creator) - University of Southern Denmark
Publication Details: PLoS ONE, Vol.9(7), e102126
Publisher: Public Library of Science
Identifiers: 991005540009007891
Copyright: © 2014 Poongavanam et al.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 2 Chemistry; 2.170 Nucleic Acids Chemistry; 2.170.988 Oligonucleotide Modifications
Web Of Science research areas: Biochemistry & Molecular Biology
ESI research areas: Biology & Biochemistry