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Updated: Jul 20, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Conformational stability and order of Hoogsteen base pair induced by protein binding
Kanika Kole1, Aayatti Mallick Gupta1, Jaydeb Chakrabarti1
1Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
Abstract:
Several experimental studies have shown that Hoogsteen (HG) base pair (bp) stabilizes in the presence of proteins. The molecular mechanism underlying this stabilization is not well known. This leads us to examine the stability of the HG bp in duplex DNA using all-atom molecular dynamics simulation in both the absence and presence of proteins. We use conformational thermodynamics to investigate the stability of a HG bp in duplex DNA at the molecular level. We compute the changes in the conformational free energy and entropy of DNA when DNA adopts a HG bp in its bp sequence rather than a Watson-Crick (WC) bp in both naked DNA and protein-bound DNA complex. We observe that the presence of proteins stabilizes and organizes the HG bp and the entire DNA duplex. Sugar-phosphate, sugar-base, and sugar-pucker torsion angles play key roles in stabilizing and ordering the HG bp in the protein-bound DNA complex.
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