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Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Unfolding Thermodynamics of DNA Kissing-Loop Interactions

Kissing-loop interactions (KLI) are common biological motifs found in RNA-RNA interactions. While significant computational work has been done on the thermodynamics and structure of RNA kissing-loop interactions, there are only a few experimental studies on the thermodynamics of kissing and none give complete and detailed thermodynamic reports. As a proof of concept, we modeled a monomolecular and bimolecular KLI and determined a complete thermodynamic description of the folding/unfolding of an intramolecular DNA kissing complex (Kissing Complex), two bimolecular kissing complexes (KHp1 + KHp2, KS1 + KS2), a non-kissing control complex (No Kiss Com) and their appropriate control stem-loop motifs (KHp1, KHp2, TLKHp2). We also tested the ability of the kissing complex to engage in kissing when sterically strained by adding a complementary strand to the base. The transition temperature of each oligonucleotide remains constant over a ten-fold range of total strand concentration, indicating all molecules formed intramolecularly, with the exception of KHp2, which displayed two transitions, one bimolecular and one monomolecular which was attributed to the formation of a duplex. Kissing Complex unfolded triphasically, with the last two peaks corresponding to the two hairpins that make up the kissing complex and the first peak corresponding to the KLI (ΔHcal = 23.7 kcal/mol). No Kiss Com unfolded biphasically, with two peaks corresponding to the two individual hairpins that make up the complex, but no peak relating to a KLI, indicating that we are indeed able to detect the thermodynamics of a KLI. The two bimolecular kissing complexes also displayed KLI but only at high concentrations. Addition of the complementary strand to the base of Kissing Complex abolished the KLI while maintaining integrity of the individual hairpin stems.

This research has been supported by Grant MCB-1122029 from NSF.

Carolyn E. Carr
Luis A. Marky

Department of Pharmaceutical Sciences
University of Nebraska Medical Center
Omaha, NE 68198-6025

Ph: (402) 559-4628
Fx: (402) 559-9543
Email: lmarky@unmc.edu