Unique Length-Dependent Biophysical Properties of Repetitive DNA

Expansion of a trinucleotide repeat (TNR) sequence is the molecular signature of several neurological disorders. The formation of noncanonical structures by the TNR sequence is proposed to contribute to the expansion mechanism. Furthermore, it is known that the propensity for expansion increases with repeat length. In this work, we use calorimetry to describe the thermodynamic parameters (Delta H, T Delta S, and Delta G) of the noncanonical stem-loop hairpins formed by the TNR sequences (CAG)(n) and (CTG)(n), as well as the canonical (CAG)(n)/(CTG)(n) duplexes, for n = 6-14. Using a thermodynamic cycle, we calculated the same thermodynamic parameters describing the process of converting from noncanonical stem loop hairpins to a canonical duplex. In addition to these thermodynamic analyses, we used spectroscopic techniques to determine the rate at which the noncanonical structures convert to duplex and the activation enthalpy Delta H-double dagger describing this process. We report that the thermodynamic parameters of unfolding the stem-loop (CTG)(n) and (CAG)(n) hairpins, along with the thermodynamic and kinetic properties of hairpin to duplex conversion, do not proportionally correspond to the increase in length, but rather show a unique pattern that depends on whether the sequence has an even or odd number of repeats.