title: Distribution of distances between DNA barcode labels in nanochannels close to the persistence length.
abstract: We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension.
authors: Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors: Wesley F
authors: WF
authors: Reinhart
authors: BioNano Genomics, 9640 Towne Centre Dr., Ste. 100, San Diego, California 92121, USA.
authors: Jeff G
authors: JG
authors: Reifenberger
authors: Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors: Damini
authors: D
authors: Gupta
authors: Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors: Abhiram
authors: A
authors: Muralidhar
authors: Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors: Julian
authors: J
authors: Sheats
authors: BioNano Genomics, 9640 Towne Centre Dr., Ste. 100, San Diego, California 92121, USA.
authors: Han
authors: H
authors: Cao
authors: Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors: Kevin D
authors: KD
authors: Dorfman
mesh_terms: D002874:Chromosome Mapping; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D005456:Fluorescent Dyes / Q000737:chemistry; D016680:Genome, Bacterial / Q000235:genetics; D036103:Nanotechnology / Q000379:methods*; D011336:Probability
chemical_list: D004269:DNA, Bacterial; D005456:Fluorescent Dyes