Schedule May 27, 2011
Bandpass Filtering of DNA Elastic Modes Using Confinement and Tension
Jun Lin (UCSB)

Jun Lin1, Fredrik Persson3, Joachim Fritzsche3, Jonas O. Tegenfeldt3, and Omar A. Saleh1,2
1BMSE Program
2Materials Department, University of California, Santa Barbara, CA (USA)
3Physics Department, University of Gothenburg, Goteborg (Sweden)

During a variety of biological and technological processes, biopolymers are simultaneously subject to both confinement and external forces. While significant efforts have gone into understanding the physics of polymers that are only confined [1-3], or only under tension [4-7], little work has been done to explore the effects of the interplay of force and confinement. Here, we study the combined effects of stretching and confinement on a polymer's configurational freedom. We measure the elastic response of long double-stranded DNA molecules that are partially confined to thin, nanofabricated slits. We account for the data through a model in which the DNA's short wavelength transverse elastic modes are cut off by applied force and the DNA's bending stiffness (as in the Marko-Siggia model [5]), while long-wavelength modes are cut off by confinement. Thus, we show that confinement and stretching combine to permit tunable bandpass filtering of the elastic modes of long polymers.

[1] Odijk, T. “The statistics and dynamics of confined or entangled stiff polymers”, Macromolecules, vol: 16, 1983.
[2] de Gennes, P. G. “Scaling concepts in polymer physics” Cornell University Press, 1979.
[3] Persson F. & Tegenfeldt J. O. “DNA in nanochannels-directly visualizing genomic information”. Chem. Soc. Rev., vol: 39, 2010.
[4] Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. “Entropic elasticity of lambda-phage DNA”. Science, vol: 265, 1994.
[5] Marko, J. F. & Siggia, E. D. “Stretching DNA”. Macromolecules vol: 28, 1995. [6] Pincus, P. “Excluded volume effects and stretched polymer-chains”. Macromolecules, vol: 9, 1976.
[7] Saleh, O. A., McIntosh, D. B., Pincus, P. & Ribeck, N. “Nonlinear low force elasticity of single-stranded DNA molecules”. Phys. Rev. Lett., vol: 102, 2009.

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