Abstract
DNA intramolecular hairpins are appropriate models for the thermodynamic description of the pseudo-intramolecular melting behavior of native DNA. To improve our understanding of the stability and melting behavior of DNA secondary structures and of the physical properties of nucleic acids, we have carried out a thermodynamic investigation of all possible bulges and mismatches in the hairpin molecule: d(GCNGCT5GCGC) and d(GCNGCT5GCMGC), where N represents a bulged base and N-M represents a W-C or mismatched base pair. We used circular dichroism spectroscopy to determine the overall conformation of each hairpin and UV melting and differential scanning calorimetry techniques to characterize their unfolding thermodynamics. The majority of hairpins melted in two-state monophasic transitions with transition temperatures independent of strand concentration. Relative to the host hairpin with 4 dG-dC base pairs in the stem, all hairpins with a bulge or a mismatch are less stable, while the hairpins with an extra c...
Published Version
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