Energy Landscapes of Nucleic Acid Folding and Assembly

Abstract

Theoretical and Computational Approaches to Nucleic Acid Folding, Interaction, and Assembly. The energy landscape framework offers a powerful lens for understanding how DNA and RNA fold, interact, and assemble. Readers will encounter theoretical and computational approaches for mapping these landscapes encompassing the electrostatic and solvent forces that shape nucleic acid structure to the role of ions in RNA energetics and methods for sampling RNA conformational ensembles. Chapters span scales ranging from base-pair dynamics and hairpin folding to chromatin organization and genome-level modeling and explore how multivalent protein binding reshapes nucleic acid landscapes. Thus, researchers and graduate students across physical and biophysical chemistry, computational chemistry, and molecular biophysics will gain both a conceptual foundation and computational perspectives for understanding nucleic acid structure, dynamics, folding, and function across molecular to genomic scales.