Title: Single Molecule FRET Observations of Folding for DNA Hairpins Containing Trinucleotide Repeats

Abstract: Expansions of tracks of Trinucleotide Repeats (TR) in DNA is associated with disorders including Huntington disease, fragile X syndrome and myotonic dystrophy. Unusual TR conformations may cause mutagenic DNA replication and affect downstream protein translation changes. We have used single-molecule FRET (smFRET) to study the dynamics of DNA containing repeated Cytosine-Adenine-Guanine (CAG) triplet patterns that can self-assemble into loops and hairpins. Thermodynamic characteristics such as transitional entropy and enthalpy acquired from studies of single molecules are compared with results from DNA melting bulk analysis. We have found complex patterns of hairpin stability and cooperatively that depend sensitively on the number of triplet repeats.