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Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy

  • Lennart Nilsson
  • Alessandra VillaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2036)

Abstract

Molecular dynamics simulations with a state-of-the-art force field provide an atomistic detailed description of the structural and thermodynamic features of biomolecules. Effects of chemical modifications and of the environment such as sequence, solvent, and ionic strength can explicitly be taken into account. Molecular simulation techniques can also provide insight in change in binding affinity, in protonation (pKa shift) and tautomeric propensity due to changes in the environment or in the molecular system. The quality and reliability of a simulation depend on the quality of the force field and on the reproducibility of the data, and validation depends on the availability of suitable experimental data. Here, we describe the workflow to investigate oligonucleotide hybrids using molecular simulation including hardware and software information.

Key words

Molecular dynamics simulation Force fields Structural analysis Free energy calculation pKa shift and tautomerism 

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden

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