Abstract
Many native nucleic acid hairpins contain various non-canonical structures, including mismatches, bubbles and loops. The thermodynamic landscape of these hairpins containing these motifs are not well understood. We combine optical tweezers with an energy based model to reconstruct the energy landscape for DNA hairpin unfolding. Overall hairpin stability, and the unfolding kinetics show the destabilizing effects of non-canonical elements in DNA hairpin structure. Finally, the stabilizing effect of the rhodium coordination complex [Rh(bpy)2(chrysi)]3+ is probed. Rhodium chrysi preferentially binds to defects and mismatches in hairpin stems, enhancing duplex stability. Rhodium chrysi binding thus allows interrupted hairpins to resemble fully formed ones.
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