Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations.

Vasanthanathan Poongavanam,Rakesh N Veedu,Praveen K Madala,Torben Højland,Freddie Salsbury

doi:10.1371/journal.pone.0102126

Vasanthanathan Poongavanam, Rakesh N Veedu + Show 3 more

Open Access

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

Copy DOI

Journal: PloS one	Publication Date: Jul 18, 2014
Citations: 31	License type: CC BY 4.0

Affiliation: University of Southern Denmark, University of Queensland

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.

Highlights

Aptamers constitute a class of oligonucleotides selected from a large library pool against a specific target of interest [1,2,3,4,5]
Validation of docking simulations Reproducing the crystallographically observed conformation of the ligand is a minimum requirement to determine whether a docking setup is applicable to a given system
To investigate more about these findings, first we have developed the models using the RB69 and KOD DNA polymerase-DNA crystal structure in which the terminal nucleotide on the primer DNA strand was structurally modified to an locked nucleic acid (LNA) nucleotide in order to understand how this change effects the incoming LNA-TTP and dTTP orientation within the active site

Summary

Introduction

Aptamers constitute a class of oligonucleotides selected from a large library pool against a specific target of interest [1,2,3,4,5]. Aptamers containing natural DNA or RNA nucleotides have some serious limitations like poor nuclease resistance (low biostability) and low target binding affinity. Locked nucleic acid (LNA) is one of the most prominent and successful among these analogues and is used extensively for various applications in chemical biology [8,9,10,11]. LNA offers unique properties needed for successful therapeutic application of oligonucleotides such as high binding affinity to complementary DNA and RNA oligonucleotides and high stability in biological systems, ie. The usefulness of LNA-modified oligonucleotides for various applications has been the subject for many scientific investigations [10,11]. 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

Methods

Results

Conclusion