The modulation of DNA helical stability and geometry by the sequence and asymmetry of internal loops

Abstract

Localized domains of unpaired nucleotides can arise in DNA and RNA through several pathways, including inherent sequence, processing errors, and protein interactions. For catalytic nucleic acids and DNA nanostructures, these domains have critical roles that include serving as functional sites and positioning helical domains; however, these unpaired domains can impart genomic instability as in the trinucleotide repeat disorders. Here, we present findings from experimental and computational work that address the role of DNA internal loop characteristics (sequence, size, and asymmetry) on the energetics and structural dynamics of loop-containing helical domains.