Elongational-flow-induced scission of DNA nanotubes in laminar flow
- Creators
- Hariadi, Rizal F.
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Yurke, Bernard
Abstract
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.
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.Attached Files
Published - Hariadi2010p11757Phys_Rev_E.pdf
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Additional details
- Eprint ID
- 20727
- Resolver ID
- CaltechAUTHORS:20101109-091900905
- NNG06GAOG
- NASA
- DMS-0506468
- NSF
- EMT-0622254
- NSF
- NIRT-0608889
- NSF
- Caltech Center of Biological Circuit Design
- Created
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2010-11-23Created from EPrint's datestamp field
- Updated
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2021-11-09Created from EPrint's last_modified field