Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements

Houyin Zhang*, John F Marko

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

46 Scopus citations

Abstract

Single-DNA stretching and twisting experiments provide a sensitive means to detect binding of proteins, via detection of their modification of DNA mechanical properties. However, it is often difficult or impossible to determine the numbers of proteins bound in such experiments, especially when the proteins interact nonspecifically (bind stably at any sequence position) with DNA. Here we discuss how analogs of the Maxwell relations of classical thermodynamics may be defined and used to determine changes in numbers of bound proteins, from measurements of extension as a function of bulk protein concentration. We include DNA twisting in our analysis, which allows us to show how changes in torque along single DNA molecules may be determined from measurements of extension as a function of DNA linking number. We focus on relations relevant to common experimental situations (e.g., magnetic and optical tweezers with or without controlled torque or linking number). The relation of our results to Gibbs adsorption is discussed.

Original languageEnglish (US)
Article number031916
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume77
Issue number3
DOIs
StatePublished - Mar 18 2008

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics

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