Interaction of DNA intramolecular structures with their complementary strands: A thermodynamic approach for the control of gene expression

Irine Khutsishvili, Sarah E. Johnson, Calliste Reiling, Iztok Prislan, Hui Ting Lee, Luis A Marky

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Abstract

The folding of mRNA sequences into secondary/tertiary structures plays an important role in RNA and DNA function and expression. Disruption of these structures can potentially be used in the control of gene expression. However, a detailed understanding of the physicochemical properties of nucleic acid structures is needed before this targeting approach can be used. In this chapter, we have examined six intramolecular DNA structures and have investigated their reaction thermodynamics with single strands partially complementary to their stems and loops. We measured the heat of each reaction directly using isothermal titration calorimetry. These are compared with the heat measured indirectly using Hess cycles obtained from differential scanning calorimetric unfolding thermodynamic profiles. Each reaction yielded favorable free energy terms that were enthalpy driven, indicating each complementary strand was able to disrupt the intramolecular complex. In short, we have developed a thermodynamic approach that can be used in the control of gene expression that targets the loops of secondary structures formed by mRNA.

Original languageEnglish (US)
Title of host publicationChemical Biology of Nucleic Acids
Subtitle of host publicationFundamentals and Clinical Applications
PublisherSpringer Berlin Heidelberg
Pages367-383
Number of pages17
ISBN (Electronic)9783642544521
ISBN (Print)9783642544514
DOIs
StatePublished - Jan 1 2014

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Thermodynamics
Gene expression
Gene Expression
DNA
Hot Temperature
Messenger RNA
Calorimetry
Titration
Nucleic Acids
Free energy
Enthalpy
RNA
Scanning

Keywords

  • Antisense
  • Heat
  • Targeting DNA secondary structures
  • Thermodynamics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Khutsishvili, I., Johnson, S. E., Reiling, C., Prislan, I., Lee, H. T., & Marky, L. A. (2014). Interaction of DNA intramolecular structures with their complementary strands: A thermodynamic approach for the control of gene expression. In Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications (pp. 367-383). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-54452-1_20

Interaction of DNA intramolecular structures with their complementary strands : A thermodynamic approach for the control of gene expression. / Khutsishvili, Irine; Johnson, Sarah E.; Reiling, Calliste; Prislan, Iztok; Lee, Hui Ting; Marky, Luis A.

Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications. Springer Berlin Heidelberg, 2014. p. 367-383.

Research output: Chapter in Book/Report/Conference proceedingChapter

Khutsishvili, I, Johnson, SE, Reiling, C, Prislan, I, Lee, HT & Marky, LA 2014, Interaction of DNA intramolecular structures with their complementary strands: A thermodynamic approach for the control of gene expression. in Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications. Springer Berlin Heidelberg, pp. 367-383. https://doi.org/10.1007/978-3-642-54452-1_20
Khutsishvili I, Johnson SE, Reiling C, Prislan I, Lee HT, Marky LA. Interaction of DNA intramolecular structures with their complementary strands: A thermodynamic approach for the control of gene expression. In Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications. Springer Berlin Heidelberg. 2014. p. 367-383 https://doi.org/10.1007/978-3-642-54452-1_20
Khutsishvili, Irine ; Johnson, Sarah E. ; Reiling, Calliste ; Prislan, Iztok ; Lee, Hui Ting ; Marky, Luis A. / Interaction of DNA intramolecular structures with their complementary strands : A thermodynamic approach for the control of gene expression. Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications. Springer Berlin Heidelberg, 2014. pp. 367-383
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