Modeling multiple duplex DNA attachments in a force-extension experiment

Allan Raudsepp; Martin A K Williams; Geoffrey B Jameson

doi:10.1016/j.bpr.2022.100045

Modeling multiple duplex DNA attachments in a force-extension experiment

Biophys Rep (N Y). 2022 Feb 2;2(1):100045. doi: 10.1016/j.bpr.2022.100045. eCollection 2022 Mar 9.

Authors

Allan Raudsepp¹, Martin A K Williams^{1

2}, Geoffrey B Jameson^{1

2}

Affiliations

¹ School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
² MacDiarmid Institute, Victoria University of Wellington, Wellington, New Zealand.

Abstract

Optical tweezers-based DNA stretching often relies on tethering a single end-activated DNA molecule between optically manipulated end-binding beads. Measurement success can depend on DNA concentration. At lower DNA concentrations tethering is less common, and many trials may be required to observe a single-molecule stretch. At higher DNA concentrations tethering is more common; however, the resulting force-extensions observed are more complex and may vary from measurement to measurement. Typically these more complex results are attributed to the formation of multiple tethers between the beads; however, to date there does not appear to have been a critical examination of this hypothesis or the potential usefulness of such data. Here we examine stretches at a higher DNA concentration and use analysis and simulation to show how the more complex force-extensions observed can be understood in terms of multiple DNA attachments.