Pulling geometry induced errors in single molecule force spectroscopy measurements

¹ Duke University

^* To whom correspondence should be addressed. E-mail: pemar{at}duke.edu.

Submitted on January 19, 2007
Revised on February 3, 2007
Accepted on 13 February 2007

	Abstract

In AFM-based single molecule force spectroscopy, it is tacitly assumed that the pulling direction coincides with the end-to-end vector of the molecule fragment being stretched. By systematically varying the position of the attachment point on the substrate relative to the AFM tip, we investigate empirically and theoretically the effect of the pulling geometry on force-extension characteristics of double-stranded DNA. We find that increasing the pulling angle can significantly lower the force of the characteristic overstretching transition and increase the width of the plateau feature beyond the canonical 70%. These effects, when neglected, can adversely affect the interpretation of measured force-extension relationships. We quantitatively evaluate force and extension errors originating from this "pulling angle effect" and stress the need to correct the pulling geometry when stretching rigid molecules with an AFM.

Key Words: Atomic force spectroscopy (AFM), DNA, Pulling angle effect, Single molecule force spectroscopy

This article has been cited by other articles:

				M. Rivera, W. Lee, C. Ke, P. E. Marszalek, D. G. Cole, and R. L. Clark Minimizing Pulling Geometry Errors in Atomic Force Microscope Single Molecule Force Spectroscopy Biophys. J., October 15, 2008; 95(8): 3991 - 3998. [Abstract] [Full Text] [PDF]

				Y. Seol, J. Li, P. C. Nelson, T. T. Perkins, and M. D. Betterton Elasticity of Short DNA Molecules: Theory and Experiment for Contour Lengths of 0.6 7 {micro}m Biophys. J., December 15, 2007; 93(12): 4360 - 4373. [Abstract] [Full Text] [PDF]