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Biomicrofluidics / Volume 6 / Issue 1 / REGULAR ARTICLES

Biomicrofluidics 6, 014101 (2012); http://dx.doi.org/10.1063/1.3672691 (9 pages)

Resolution limit for DNA barcodes in the Odijk regime

Yanwei Wang1,2, Wes F. Reinhart2, Douglas R. Tree2, and Kevin D. Dorfman2

1Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou 215123, People’s Republic of China
2Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA

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(Received 9 November 2011; accepted 6 December 2011; published online 3 January 2012)

We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of the DNA, simulations indicate that the theoretical predictions are reasonably accurate for channel widths up to two-thirds of the persistence length. Our results quantify the conjecture that DNA barcoding has kilobase pair resolution—provided the nanochannel lies in the Odijk regime.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THEORY
  3. SIMULATION METHOD
  4. RESULTS AND DISCUSSION
  5. CONCLUDING REMARKS

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KEYWORDS and PACS

Keywords

bioinformatics, DNA, molecular biophysics, Monte Carlo methods

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3672691

PUBLICATION DATA

ISSN

1932-1058 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
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    T. Odijk, Phys. Rev. E 77, 060901(R) (2008).

    P. Cifra, J. Chem. Phys. 131, 224903 (2009)JCPSA6000131000022224903000001.


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