Thermodynamic contributions for the inclusion of bulges and mismatches in dna hairpin loops

Ronald Shikiya, Luis A. Marky

Research output: Chapter in Book/Report/Conference proceedingChapter


Bulges and mismatches in DNA can promote frame-shift and translational/transversional mutations, respectively. A complete characterization of the effects that bulges and mismatches have on duplex stability is required to understand the mechanisms of mutations. In this work, we used a combination of temperature-dependent UV spectroscopy, differential scanning calorimetry and circular dichroism techniques to investigate the thermodynamic contribution and conformation for the incorporation of bulges and mismatches in duplex DNA. Specifically, we obtained standard thermodynamic profiles (δG, δH, and δS) for the helix-coil transition of a host DNA hairpin-loop with sequence d(GTAGCT5GCTAC), T5 is a loop of 5 thymines; and hairpins containing one of the four potential bulges (dC, dT, dA, or dG) and/or one of the homo-mismatches (dC-dC, dT-dT, dA-dA, or dG-dG) in two base-pair stack environments (TA/TA and AG/CT) located in the stem of the host hairpin. All hairpins melted in two-state monophasic transitions with transition temperatures, TM, independent of strand concentration, which is consistent with their intramolecular formation. Their CD spectra indicated all hairpins folded in the "B" conformation. However, the incorporation of a lesion resulted in lower thermal (δTM = 6.6 to 24.7 C) and thermodynamic (δδG = 0.1 to 3.0 kcal/mol) stabilities, due to lower enthalpies (δδH = 0.2 to 14.7 kcal/mol), indicating a loss of base-pair stacking interactions. Overall, bulges cause higher destabilization than mismatches. Lesions incorporated in the AG/CT environment generated slightly larger destabilization effect relative to the TA/TA environment. The results show that cytosine lesions destabilized the most followed by adenine lesions, thymine lesions, and guanine lesions.

Original languageEnglish (US)
Title of host publicationA Closer Look at Calorimetry
PublisherNova Science Publishers, Inc.
Number of pages30
ISBN (Electronic)9781536157901
ISBN (Print)9781536157895
StatePublished - Jun 5 2019

ASJC Scopus subject areas

  • Chemistry(all)


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