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Hook Formation of Electrically Driven DNA Collisions with Finite-Sized Obstacles

Published online by Cambridge University Press:  01 February 2011

Greg C. Randall  and
Patrick S. Doyle
Greg C. Randall
Affiliation:
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
Patrick S. Doyle
Affiliation:
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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Abstract

We present a comprehensive study of the hooking mechanism of a single DNA molecule in electrophoretic motion colliding with a single microfabricated obstacle. During a collision, DNA impacts an obstacle and deforms. The impact conditions dictate whether this collision results in a “roll-off” event or “hooking” event. Our objective is to better understand the physics of a collision. Specifically, we note that a finite-sized insulating obstacle induces local electric field gradients that can enhance the size-dependent hooking probability. We validate that the hooking mechanism is analogous to a polymer in a transient, non-homogeneous elongational field with a strength characterized by the Deborah number, De. We then show that hook formation increases with De for finite-sized obstacles in the regime De<40.

Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 790: Symposium P – Dynamics in Small Confining Systems–2003 , 2003 , P3.3
Copyright
Copyright © Materials Research Society 2004

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References

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