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Presentation date

Summer 8-10-2022

College, Institute, or Department

Pharmaceutical Sciences

Faculty Mentor

Luis A. Marky

Research Mentor

Luis A. Marky


The global stability of DNA molecules depends on base stacking, base-pairing, ionic and hydration contributions. To understand the mechanisms that govern the many biological roles of nucleic acids, it is essential to have a complete physical description of the folding of nucleic acids, including ion and water binding. We used a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry to investigate the effect of the loop length on the unfolding thermodynamics of a set of DNA stem-loop motifs with the following sequence: d(5’-GCGCUnGCGC), where n = 3, 5, 7, and 9.

The folding of each hairpin loop resulted in a monophasic transition that was monomolecular. The favorable folding of each hairpin (negative ∆Go) in this set resulted in a thermodynamic compensation of a favorable enthalpy with an unfavorable entropy contributions, enthalpy contributions correspond to formation of base-pair stackings while the unfavorable entropy contributions correspond mainly to the immobilization of counterions, as the length of the uracil hairpin loop increases, the stability of the hairpin decreases (the free energy term becomes more positive), due to a less favorable entropic contribution because more counterions are binding. Relative to a similar set of thymine hairpin loops, we measured less favorable free energy terms because of the lower thermal stability of the uracil hairpins (lower TM’s) and their lesser impact of ion binding. Supported by Grant MCB-1912587 from the NSF.


Uracil, Thymine, Thermodynamics, Calorimetry, UV/Vis, Spectrophotometry

Thermodynamic Contributions of Deoxyuridine Loops to the Folding of DNA Straight Hairpin Loops with d(GCGC/GCGC) Stems