Linked Life Data

21423606

Source:http://linkedlifedata.com/resource/pubmed/id/21423606

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2011-3-22
pubmed:abstractText
We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50-100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in ~100 nm channels, we observe a critical length scale ~10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150-250 nm, separated by ~10 m exist in the confined DNA during the transition between the two regimes. For ~50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-12524271, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-16090189, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-17144737, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-17175538, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-17766363, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-17930801, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-18340435, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-18851263, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-18851496, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-19049008, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-19072931, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-20179820, http://linkedlifedata.com/resource/pubmed/commentcorrection/21423606-20699272
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1932-6203
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
6
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
e16890
pubmed:dateRevised
2011-7-27
pubmed:meshHeading
pubmed:year
2011
pubmed:articleTitle
Transition between two regimes describing internal fluctuation of DNA in a nanochannel.
pubmed:affiliation
Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't