The size of internal loops influences the unfolding thermodynamics of DNA hairpins

Iztok Prislan, Hui Ting Lee, Cynthia Lee, Luis A. Marky

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations


The main focus is to further our understanding of the physico-chemical properties of unusual DNA structures. We designed a set of stem-loop DNA molecules to mimic a common motif of mRNA i.e., a hairpin with internal loops. We used a combination of UV spectroscopy and differential scanning calorimetry (DSC) techniques to determine the unfolding thermodynamics of a set of hairpins with sequence: d(GCGCTnGTAACT5GTTACTnGCGC), where "Tn" corresponds to internal loops with n = 1, 3 or 5 and "T5" is an end loop of 5 thymines. UV melts of each hairpin show monophasic transitions with TMs that are independent of strand concentration i.e., all hairpins formed intramolecularly. DSC profiles indicate hairpin unfolding results from the typical compensation of an unfavorable enthalpy with a favorable entropy. The increase in the size of the internal loop yielded: a) lower TMs and similar enthalpy contributions; b) lower heat capacity values that correlated with the lower releases of structural water; and c) higher ion releases. Therefore, hairpin loops with large internal loops are less stable and amenable for their targeting with complementary oligonucleotides.

Original languageEnglish (US)
Title of host publicationFrontiers in Nucleic Acids
PublisherAmerican Chemical Society
Number of pages18
ISBN (Print)9780841226234
StatePublished - Oct 25 2011

Publication series

NameACS Symposium Series
ISSN (Print)0097-6156
ISSN (Electronic)1947-5918

ASJC Scopus subject areas

  • General Chemistry
  • General Chemical Engineering


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