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 Citations (Scopus)

Abstract

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
Pages93-110
Number of pages18
ISBN (Print)9780841226234
DOIs
StatePublished - Oct 25 2011

Publication series

NameACS Symposium Series
Volume1082
ISSN (Print)0097-6156
ISSN (Electronic)1947-5918

Fingerprint

Differential scanning calorimetry
Enthalpy
DNA
Thermodynamics
Thymine
Oligonucleotides
Ultraviolet spectroscopy
Chemical properties
Specific heat
Entropy
Ions
Messenger RNA
Molecules
Water
Compensation and Redress

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)

Cite this

Prislan, I., Lee, H. T., Lee, C., & Marky, L. A. (2011). The size of internal loops influences the unfolding thermodynamics of DNA hairpins. In Frontiers in Nucleic Acids (pp. 93-110). (ACS Symposium Series; Vol. 1082). American Chemical Society. https://doi.org/10.1021/bk-2011-1082.ch006

The size of internal loops influences the unfolding thermodynamics of DNA hairpins. / Prislan, Iztok; Lee, Hui Ting; Lee, Cynthia; Marky, Luis A.

Frontiers in Nucleic Acids. American Chemical Society, 2011. p. 93-110 (ACS Symposium Series; Vol. 1082).

Research output: Chapter in Book/Report/Conference proceedingChapter

Prislan, I, Lee, HT, Lee, C & Marky, LA 2011, The size of internal loops influences the unfolding thermodynamics of DNA hairpins. in Frontiers in Nucleic Acids. ACS Symposium Series, vol. 1082, American Chemical Society, pp. 93-110. https://doi.org/10.1021/bk-2011-1082.ch006
Prislan I, Lee HT, Lee C, Marky LA. The size of internal loops influences the unfolding thermodynamics of DNA hairpins. In Frontiers in Nucleic Acids. American Chemical Society. 2011. p. 93-110. (ACS Symposium Series). https://doi.org/10.1021/bk-2011-1082.ch006
Prislan, Iztok ; Lee, Hui Ting ; Lee, Cynthia ; Marky, Luis A. / The size of internal loops influences the unfolding thermodynamics of DNA hairpins. Frontiers in Nucleic Acids. American Chemical Society, 2011. pp. 93-110 (ACS Symposium Series).
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