Chapter 13 Thinking Inside the Box. Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding

Nathan A. Siegfried, Philip C. Bevilacqua

Research output: Chapter in Book/Report/Conference proceedingChapter

18 Citations (Scopus)

Abstract

Double and triple mutant thermodynamic cycles provide a means to dissect the cooperativity of RNA and DNA folding at both the secondary and tertiary structural levels through use of the thermodynamic box or cube. In this article, we describe three steps for applying thermodynamic cycles to nucleic acid folding, with considerations of both conceptual and experimental features. The first step is design of an appropriate system and development of hypotheses regarding which residues might interact. Next is implementing this design in terms of a tractable experimental strategy, with an emphasis on UV melting. The final step, and the one we emphasize the most, is interpreting mutant cycles in terms of coupling between specific residues in the RNA or DNA. Coupling free energy in the absence and presence of changes elsewhere in the molecule is discussed in terms of specific folding models, including stepwise folding and concerted changes. Last, we provide a practical section on the use of commercially available software (KaleidaGraph) to fit melting data, along with a consideration of error propagation. Along the way, specific examples are chosen from the literature to illustrate the methods. This article is intended to be accessible to the biochemist or biologist without extensive thermodynamics background.

Original languageEnglish (US)
Title of host publicationBiothermodynamics, Part A
EditorsMichael Johnson, Jo Holt, Gary Ackers
Pages365-393
Number of pages29
EditionA
DOIs
StatePublished - Mar 16 2009

Publication series

NameMethods in Enzymology
NumberA
Volume455
ISSN (Print)0076-6879

Fingerprint

RNA Folding
Thermodynamics
RNA
DNA
Freezing
Melting
Nucleic Acids
Free energy
Software
Molecules

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

Siegfried, N. A., & Bevilacqua, P. C. (2009). Chapter 13 Thinking Inside the Box. Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding. In M. Johnson, J. Holt, & G. Ackers (Eds.), Biothermodynamics, Part A (A ed., pp. 365-393). (Methods in Enzymology; Vol. 455, No. A). https://doi.org/10.1016/S0076-6879(08)04213-4
Siegfried, Nathan A. ; Bevilacqua, Philip C. / Chapter 13 Thinking Inside the Box. Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding. Biothermodynamics, Part A. editor / Michael Johnson ; Jo Holt ; Gary Ackers. A. ed. 2009. pp. 365-393 (Methods in Enzymology; A).
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Siegfried, NA & Bevilacqua, PC 2009, Chapter 13 Thinking Inside the Box. Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding. in M Johnson, J Holt & G Ackers (eds), Biothermodynamics, Part A. A edn, Methods in Enzymology, no. A, vol. 455, pp. 365-393. https://doi.org/10.1016/S0076-6879(08)04213-4

Chapter 13 Thinking Inside the Box. Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding. / Siegfried, Nathan A.; Bevilacqua, Philip C.

Biothermodynamics, Part A. ed. / Michael Johnson; Jo Holt; Gary Ackers. A. ed. 2009. p. 365-393 (Methods in Enzymology; Vol. 455, No. A).

Research output: Chapter in Book/Report/Conference proceedingChapter

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