Shear Unzipping of DNA
Original entry: Naveen Sinha, APPHY 226, Spring 2009
Second Entry: Nick Chisholm, AP 225, Fall 2009 (In Progress)
Shear Unzipping of DNA
Buddhapriya Chakrabarti, David R. Nelson
The Journal of Physical Chemistry B 113 (12), 3831-3836 (2009).
Soft matter keywords:
deGennes, polymer, shear
Biologists have already investigated the helical unzipping of DNA, which occurs during DNA replication and other biological processes (see Fig. 1b). However, the problem of shear-induced unzipping in such systems (see Fig. 1a) has yet to be investigated. Although not as prevalent in biological systems, it is directly relevant to artificially constructed nanostructures that are bound together with DNA duplexes. The shear situation is different from the helical one because the stress is distributed throughout the length of the DNA, rather than at just the bond nearest the end.
Soft Matter Aspects
When studying an analogous system, deGennes used the model of a ladder connected by harmonic springs. This led to the prediction of a linear increase in the minimal force needed to unzip the DNA as a function of overlap length (<math>\beta \gamma</math> and <math>\delta \epsilon</math> in Fig. 1). The model also predicted a saturation in this force above a critical DNA length. A physical version of this system has been realized by the Prentiss group, in which a double-stranded DNA is trapped between a glass capillary and a magnetic bead, which can be pulled away from the surface to stretch the DNA (i.e. the force, F, would be applied at <math>\alpha</math> and <math>\omega</math> in Fig. 1). To more accurately model this situation, the authors look at both complementary base-pair interactions on opposite strands of the DNA and next-nearest neighbor interactions, also on opposite strands. In addition, the authors look at the case of a heteropolymer, with both A-T and G-C pairs.
The authors find that most of the bond breakages occur near the endpoints, with a frequency that occurs with a characteristic length scale. The unzipping process advances in jumps and plateaus, rather than uniformly. In future work, the model could be modified to take into account the helical twist of the DNA. It would also be interesting to investigate how these findings could be applied to other heteropolymers.
written by: Naveen N. Sinha
Authors: B. Chakrabarti, and D. R. Nelson
Publication: The Journal of Physical Chemistry B 113 (12), 3831-3836 (2009)
Soft Matter Keywords
This paper is a theoretical study of shear denaturation (unzipping) of DNA. Using a microscopic Hamiltonian, the authors derive a nonlinear generalization of a ladder model of shear unzipping proposed by deGennes. Previously studied is the physics behind single molecule DNA unzipping, which is the helicase-mediated unzipping that occurs during DNA replication (see Figure 1(b)). Although the case of shear unzipping (see Figure 1(a)) is less biologically relevant, its study leads to interesting materials science applications; the authors note that these include determining the strength of DNA or gold nanoparticle assemblies.
More specifically, the authors model the sugar phosphate backbone of the DNA by Hookean springs and expand in the displacements of the nearest neighbor interactions of complementary base pairs on opposite rungs of the ladder, and the next nearest neighbor interactions on different rungs of the ladder (this is a simple model of stacking interactions). Both are expanded to quadratic order, and then the eigenmode corresponding to shear deformation is projected out, thus leading to a nonlinear Hamiltonian.
Soft Matter Discussion
 B. Chakrabarti, and D. R. Nelson, "Shear Unzipping of DNA," The Journal of Physical Chemistry B 113 (12), 3831-3836 (2009).