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The physics of DNA in nanochannels

MNE 2007
Publication Date
  • Biology
  • Mathematics


The Physics of DNA in Nanochannels The Physics of DNA in Nanochannels W. Reisner a,b,c , N. Larsen c , H. Flyvbjerg c , J.O. Tegenfeldt b , A. Kristensen a a MIC – Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, DK-2800 Denmark phone: +4528746293. e-mail: [email protected] b Department of Physics, Divison of Solid State Physics, Lund University, Lund, Box 118, S-221 00 Sweden c Danish Polymer Centre and Biosystems Department, RISØ National Laboratory, Technical University of Denmark, Roskilde, DK-4000 Denmark Key words: DNA, nanochannels, effective width, nanoconfinement Understanding the behaviour of dsDNA in confined geometries at the single-molecule level is crucial to the development of bionanofluidic technology for chip-based analysis systems. When the device dimension falls below characteristic molecular scales (e.g. the radius of gyration, persistence length), qualitatively new physical regimes are reached in which statistical properties of the macromolecule deviate from their values in bulk and become functions of the degree of confinement. When confined in effectively 1D dimensional channel structures (both height and depth in the nanoregime), DNA is observed to stretch out in such a way that the extension along the nanochannel is linearly proportional to the contour length. This proportionality establishes a one-to-one correspondence between position along the DNA and position with the genetic code that can be used to correlate the action of enzymes or fluorescent probes to specific genetic sequences. This talk will present scaling arguments and experimental data on the basic physics of DNA stretching in silica nanochannels with dimensions ranging from 400nm to 35nm, including the effect of varying device dimension and solution ionic strength. Ionic strength is observed to have a surprisingly strong effect on the extensio

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