Shear Unzipping of DNA

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Shear Unzipping of DNA

Buddhapriya Chakrabarti, David R. Nelson

The Journal of Physical Chemistry B 2009 113 (12), 3831-3836

Soft matter keywords:

deGennes, polymer, shear

Summary

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.

NelsonUnzipDNAfig1.png

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