Thermodynamics of DNA Hybridization from Atomistic Simulations

Gül H. Zerze, Frank H. Stillinger, Pablo G. Debenedetti

Research output: Contribution to journalArticlepeer-review

Abstract

Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based advanced sampling technique to calculate the free energy of hybridization, and estimate the melting temperature of DNA oligomers at atomistic resolution. The free energy landscapes are reported as a function of a native-topology-based order parameter for the Drew-Dickerson dodecamer and for a range of DNA decamer sequences of different GC content. Our estimated melting temperatures match the experimental numbers within ±15 °C. As a test of the numerical reliability of the procedures employed, it was verified that the predicted free energy surfaces and melting temperatures of the d- A nd l-enantiomers of the Drew-Dickerson dodecamer were indistinguishable within numerical accuracy.

Original languageEnglish (US)
Pages (from-to)771-779
Number of pages9
JournalJournal of Physical Chemistry B
Volume125
Issue number3
DOIs
StatePublished - Jan 28 2021

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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