Structure, stability and elasticity of DNA nanotubes

Joshi, Himanshu and Dwaraknath, Anjan and Maiti, Prabal K (2015) Structure, stability and elasticity of DNA nanotubes. In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17 (2). pp. 1424-1434.

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Abstract

DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for the construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix, 8-helix and tri-tubes with different sequences and lengths. We have used fully atomistic molecular dynamics simulations to study the structure, stability and elasticity of these structures. Several nanosecond long MD simulations give the microscopic details about DNA nanotubes. Based on the structural analysis of simulation data, we show that 6-helix nanotubes are stable and maintain their tubular structure; while 8-helix nanotubes are flattened to stabilize themselves. We also comment on the sequence dependence and the effect of overhangs. These structures are approximately four times more rigid having a stretch modulus of similar to 4000 pN compared to the stretch modulus of 1000 pN of a DNA double helix molecule of the same length and sequence. The stretch moduli of these nanotubes are also three times larger than those of PX/JX crossover DNA molecules which have stretch moduli in the range of 1500-2000 pN. The calculated persistence length is in the range of a few microns which is close to the reported experimental results on certain classes of DNA nanotubes.

Item Type:	Journal Article
Publication:	PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Publisher:	ROYAL SOC CHEMISTRY
Additional Information:	Copyright for this article belongs to the ROYAL SOC CHEMISTRY, THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	21 Jan 2015 05:28
Last Modified:	21 Jan 2015 05:28
URI:	http://eprints.iisc.ac.in/id/eprint/50712

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