ArticleThe Journal of chemical physics2015
Distribution of distances between DNA barcode labels in nanochannels close to the persistence length.
Article in The Journal of chemical physics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- FaNDOM: Fast nested distance-based seeding of optical maps.Patterns (New York, N.Y.) · 2021Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
- 3D Printing-Enabled DNA Extraction for Long-Read Genomics.ACS omega · 2020Article
- Conformation of Flexible and Semiflexible Chains Confined in Nanoposts Array of Various Geometries.Polymers · 2020Article
- Limitations of the equivalent neutral polymer assumption for theories describing nanochannel-confined DNA.Physical review. E · 2020Article
- Extension distribution for DNA confined in a nanochannel near the Odijk regime.The Journal of chemical physics · 2019Article
- Simulations corroborate telegraph model predictions for the extension distributions of nanochannel confined DNA.Biomicrofluidics · 2019Article
- Measuring the wall depletion length of nanoconfined DNA.The Journal of chemical physics · 2018Article
- Miniaturized flow cell with pneumatically-actuated vertical nanoconfinement for single-molecule imaging and manipulation.Biomicrofluidics · 2018Article
- Distribution of label spacings for genome mapping in nanochannels.Biomicrofluidics · 2018Article
- Evaluation of Blob Theory for the Diffusion of DNA in Nanochannels.Macromolecules · 2018Article
- Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel.Macromolecules · 2018Article
- One-Parameter Scaling Theory for DNA Extension in a Nanochannel.Physical review letters · 2017Article
- Sequence-Dependent Persistence Length of Long DNA.Physical review letters · 2017Article
- Article
- Erratum: "Distribution of distances between DNA barcode labels in nanochannels close to the persistence length" [J. Chem. Phys. 142, 064902 (2015)].The Journal of chemical physics · 2017Article
- Simulations of knotting of DNA during genome mapping.Biomicrofluidics · 2017Article
- OMBlast: alignment tool for optical mapping using a seed-and-extend approach.Bioinformatics (Oxford, England) · 2017Article
- Modeling the relaxation of internal DNA segments during genome mapping in nanochannels.Biomicrofluidics · 2016Article
- Nanotechnologies for biomedical science and translational medicine.Proceedings of the National Academy of Sciences of the United States of America · 2015Review
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
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.
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