Abstract
Repetitive DNA sequences exhibit complex structural and energy
landscapes, populated by metastable, non-canonical states, that favor expansion
and deletion events correlated with disease phenotypes. To probe the origins of
such genotype-phenotype linkages, we report the impact of sequence and repeat
number on properties of (CNG) repeat bulge loops. We find the stability of
duplexes with a repeat bulge loop is controlled by two opposing effects; a loop
junction-dependent destabilization of the underlying double helix, and a
self-structure dependent stabilization of the repeat bulge loop. For small bulge
loops, destabilization of the underlying double helix overwhelms any favorable
contribution from loop self-structure. As bulge loop size increases, the
stabilizing loop structure contribution dominates. The role of sequence on
repeat loop stability can be understood in terms of its impact on the opposing
influences of junction formation and loop structure. The nature of the bulge
loop affects the thermodynamics of these two contributions differently,
resulting in unique differences in repeat size dependent minima in the overall
enthalpy, entropy, and free energy changes. Our results define factors that
control repeat bulge loop formation; knowledge required to understand how this
helix imperfection is linked to DNA expansion, deletion, and disease
phenotypes.