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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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A Deep Dive into DNA Base Pairing Interactions Under Water.

Rongpeng Li, Chi H Mak

    The Journal of Physical Chemistry. B
    |June 12, 2020
    PubMed
    Summary

    Solvent interactions significantly impact DNA base pairing energetics. Specific water molecules near bases create thermodynamic resistance, influencing DNA replication fidelity.

    Area of Science:

    • Biochemistry
    • Computational Biology
    • Molecular Biophysics

    Background:

    • Base pairing is crucial for DNA structure, function, and replication fidelity.
    • Complementarity of Guanine-Cytosine (G|C) and Adenine-Thymine (A|T) pairs is traditionally attributed to hydrogen bond differences.
    • Aqueous solvent effects on base pairing energetics are significant but not fully understood.

    Purpose of the Study:

    • To quantify the solvent's contribution to the free energy of DNA base pairing.
    • To investigate the role of water molecules in the thermodynamic stability of base pairs.
    • To explore how solvent interactions influence DNA replication fidelity.

    Main Methods:

    • Large-scale Monte Carlo simulations were employed.
    • Calculated the solvent contribution to the free energy for various base pairs.

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  • Analyzed the density of water molecules adjacent to DNA bases.

    • Main Results:

    • The solvent's contribution to base pairing free energy is universally destabilizing.
    • Despite stronger direct hydrogen bonds in G|C pairs, solvent resistance is greater, resulting in a small net free energy difference (~1 kcal/mol).
    • Observed a "freezing" of water molecules in the gap between bases, compensating for unsatisfied hydrogen bonds.

    Conclusions:

    • A small number of tightly associated "near-field" water molecules dominate the solvent's resistance to base pairing.
    • Manipulating these near-field water molecules offers a potential strategy to enhance DNA replication fidelity.
    • Understanding solvent-base pair interactions is key to deciphering DNA stability and function.