Abstract
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3‐step (easy to implement) and a 1‐step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5‐methyl‐cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Highlights
Nucleic acid hybridization occurs in a variety of contexts, including biotechnology and therapeutic applications
It is of interest to design oligonucleotides that bind a DNA or RNA target sequence with high affinity and specificity, for instance using Watson-Crick base pairing with the target, or by binding as a third strand in the major groove of a target duplex, forming a triple helix
We investigate the transformation between locked ribose and deoxyribose for pyrimidine nucleotides and the associated free energy change
Summary
Nucleic acid hybridization occurs in a variety of contexts, including biotechnology and therapeutic applications. It is of interest to design oligonucleotides that bind a DNA or RNA target sequence with high affinity and specificity, for instance using Watson-Crick base pairing with the target, or by binding as a third strand in the major groove of a target duplex, forming a triple helix. To competitively bind an oligonucleotide to a target molecule, the binding affinity needs to be higher than in the prototype (DNA) duplex. This can be achieved using non-natural nucleotides, for instance with a modified backbone, which can be uncharged as in the case of peptide nucleic acids,[1] or have a ribose moiety with restricted conformational flexibility as in locked nucleic acid (LNA).[2,3]. The presence of either LNA isomer in an oligonucleotide strand enhances its binding affinity with a DNA or RNA complementary strand as indicated by an increased melting temperature,[4,5] and the melting temperature is further increased when the fraction of LNA is increased.[3,4,6] In this study, we focus on b-D-LNA (below referred to as LNA) as it is more common in bioassays
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