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Solvents

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Theoretical Model for Solvent-Induced Base Stacking Interactions in Solvent-Free DNA Simulations.

¹Departments of Chemistry and Biological Sciences, and Center of Applied Mathematical Sciences , University of Southern California , Los Angeles , California 90089 , United States.

The Journal of Physical Chemistry. B

|February 8, 2019

Summary

This summary is machine-generated.

Theoretical models capture water

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Area of Science:

Biophysics
Computational Biology
Molecular Dynamics

Background:

Nucleic acid structures are primarily influenced by water-mediated interactions.
Single-stranded (ss) DNA and RNA exist in diverse conformations in aqueous solutions.
Accurate modeling of nucleic acid behavior requires accounting for solvent effects.

Purpose of the Study:

To develop theoretical models for solvent-induced nucleobase stacking interactions.
To incorporate solvent entropy and dispersion into base stacking free energy calculations.
To validate these models using simulations of single-stranded DNA (ssDNA) sequences.

Main Methods:

Development of theoretical models for solvent effects on base stacking.
Solvent-free Monte Carlo simulations of ssDNA sequences ((dA)n and (dT)n).
Validation against experimental small-angle X-ray scattering (SAXS) data.

Main Results:

Simulated ensembles quantitatively matched experimental SAXS data.
Adenine (dA) chains exhibit significant base stacking, while thymine (dT) chains show less but non-negligible stacking.
Stacking is chain length-dependent, with longer dA chains showing increased stacking compared to dT chains.

Conclusions:

The developed models effectively capture solvent-induced stacking interactions in ssDNA.
Base stacking significantly influences ssDNA conformations, particularly in dA sequences.
Estimated A|A stacking free energy is approximately 1 kcal/mol.