Document Detail

Conformation, length, and speed measurements of electrodynamically stretched DNA in nanochannels.
MedLine Citation:
PMID:  18339746     Owner:  NLM     Status:  MEDLINE    
A method is presented to rapidly and precisely measure the conformation, length, speed, and fluorescence intensity of single DNA molecules constrained by a nanochannel. DNA molecules were driven electrophoretically from a nanoslit into a nanochannel to confine and dynamically elongate them beyond their equilibrium length for repeated detection via laser-induced fluorescence spectroscopy. A single-molecule analysis algorithm was developed to analytically model bursts of fluorescence and determine the folding conformation of each stretched molecule. This technique achieved a molecular length resolution of 114 nm and an analysis time of around 20 ms per molecule, which enabled the sensitive investigation of several aspects of the physical behavior of DNA in a nanochannel. lambda-bacteriophage DNA was used to study the dependence of stretching on the applied device bias, the effect of conformation on speed, and the amount of DNA fragmentation in the device. A mixture of lambda-bacteriophage with the fragments of its own HindIII digest, a standard DNA ladder, was sized by length as well as by fluorescence intensity, which also allowed the characterization of DNA speed in a nanochannel as a function of length over two and a half orders of magnitude.
Christian H Reccius; Samuel M Stavis; John T Mannion; Larry P Walker; H G Craighead
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2008-03-13
Journal Detail:
Title:  Biophysical journal     Volume:  95     ISSN:  1542-0086     ISO Abbreviation:  Biophys. J.     Publication Date:  2008 Jul 
Date Detail:
Created Date:  2008-06-13     Completed Date:  2008-07-10     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  273-86     Citation Subset:  IM    
School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.
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MeSH Terms
Computer Simulation
DNA / chemistry*,  ultrastructure*
Electrochemistry / methods*
Micromanipulation / methods*
Models, Chemical*
Models, Molecular
Nanotubes / chemistry*,  ultrastructure*
Nucleic Acid Conformation
Stress, Mechanical
Reg. No./Substance:
0/Quinazolines; 141974-84-7/7-methoxydeoxyvasicinone; 9007-49-2/DNA

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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