ArticleJournal of computational chemistry2017
The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.
Article in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations.Journal of chemical theory and computation · 2020Article
- Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.Journal of chemical theory and computation · 2019Article
- [Antiviral effect of hepatitis B virus S gene-specific anti-gene locked nucleic acid in transgenic mice].Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology · 2018Article
- The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.Journal of computational chemistry · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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