Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements.
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.
Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA.
Houyin
H
Zhang
John F
JF
Marko
D000327:Adsorption; D001703:Biophysics / Q000379:methods*; D002462:Cell Membrane / Q000378:metabolism; D003599:Cytoskeleton / Q000378:metabolism; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D019563:Mechanics; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D013816:Thermodynamics
D011506:Proteins; D004247:DNA