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Elongational-flow-induced scission of DNA nanotubes in laminar flow

Hariadi, Rizal F. and Yurke, Bernard (2010) Elongational-flow-induced scission of DNA nanotubes in laminar flow. Physical Review E, 82 (4). Art. No. 046307 . ISSN 1539-3755.

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The length distributions of polymer fragments subjected to an elongational-flow-induced scission are profoundly affected by the fluid flow and the polymer bond strengths. In this paper, laminar elongational flow was used to induce chain scission of a series of circumference-programmed DNA nanotubes. The DNA nanotubes served as a model system for semiflexible polymers with tunable bond strength and cross-sectional geometry. The expected length distribution of fragmented DNA nanotubes was calculated from first principles by modeling the interplay between continuum hydrodynamic elongational flow and the molecular forces required to overstretch multiple DNA double helices. Our model has no-free parameters; the only inferred parameter is obtained from DNA mechanics literature, namely, the critical tension required to break a DNA duplex into two single-stranded DNA strands via the overstretching B-S DNA transition. The nanotube fragments were assayed with fluorescence microscopy at the single-molecule level and their lengths are in agreement with the scission theory.

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Yurke, Bernard0000-0003-3913-2855
Additional Information:© 2010 The American Physical Society. Received 25 August 2009; revised manuscript received 2 May 2010; published 19 October 2010. We are indebted to Erik Winfree for generously hosting this work in his lab and for his valuable and insightful input to the project. The authors would like to thank Rebecca Schulman, Peng Yin, Damien Woods, Victor A. Beck, Elisa Franco, Zahid Yaqoob, Karthik Sarma, Saurabh Vyawahare, Nadine Dabby, Tosan Omabegho, Jongmin Kim, Imran Malik, and Michael Solomon for valuable discussions. It is our great pleasure to acknowledge the support of the NASA Astrobiology Grant No. NNG06GAOG, NSF Grants No. DMS- 0506468, No. EMT-0622254, and No. NIRT-0608889, and the Caltech Center of Biological Circuit Design grants. This work was initiated by a serendipitous observation of elongational-flow-induced fragmantation of DNA nanotubes by Harry M. T. Choi and was undertaken to facilitate the design of a fluidics system for Rebecca Schulman and Erik Winfree’s project on engineering DNA tile-based artificial life 38. The DNA nanotubes used in this experiment and their three-dimensional illustrations were generous gifts from Peng Yin. The design and manufacturing process of the PDMS microfluidic chip were assisted by the Caltech Microfluidic Foundry.
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Caltech Center of Biological Circuit DesignUNSPECIFIED
Issue or Number:4
Classification Code:PACS: 47.15.-x, 87.15.Fh, 83.50.Jf, 62.25.-g
Record Number:CaltechAUTHORS:20101109-091900905
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:20727
Deposited By: Tony Diaz
Deposited On:23 Nov 2010 21:53
Last Modified:25 Feb 2020 02:54

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