Data for: Extension distribution for DNA confined in a nanochannel near the Odijk regime
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2018-12
2018-12
2018-12
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2019-05
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Data for: Extension distribution for DNA confined in a nanochannel near the Odijk regime
Published Date
2019-09-19
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Dorfman, Kevin D.
dorfman@umn.edu
dorfman@umn.edu
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Experimental Data
Genomics Data
Programming Software Code
Abstract
DNA confinement in a nanochannel typically is understood via mapping to the confinement of an equivalent neutral polymer by hard walls. This model has proven to be effective for confinement in relatively large channels where hairpin formation is frequent. An analysis of existing experimental data for Escherichia coli DNA extension in channels smaller than the persistence length, combined with an additional dataset for lambda -DNA confined in a 34 nm wide channel, reveals a breakdown in this approach as the channel size approaches the Odijk regime of strong confinement. In particular, the predicted extension distribution obtained from the asymptotic solution to the weakly correlated telegraph model for a confined wormlike chain deviates significantly from the experimental distribution obtained for DNA confinement in the 34 nm channel, and the discrepancy cannot be resolved by treating the alignment fluctuations or the effective channel size as fitting parameters. We posit that the DNA-wall electrostatic interactions, which are sensible throughout a significant fraction of the channel cross section in the Odijk regime, are the source of the disagreement between theory and experiment. Dimensional analysis of the wormlike chain propagator in channel confinement reveals the importance of a dimensionless parameter, reflecting the magnitude of the DNA-wall electrostatic interactions relative to thermal energy, which has not been considered explicitly in the prevailing theories for DNA confinement in a nanochannel.
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The data provided here contains experimental results, all Matlab codes for statistical analysis and for generating figures in the paper.
Referenced by
Chuang, Hui-Min, Reifenberger, Jeffrey G., Bhandari, Aditya Bikram, and Kevin Dorfman. (2019). Extension distribution for DNA confined in a nanochannel near the Odijk regime. J. Chem. Phys. 151, 114903
https://doi.org/10.1063/1.5121305
Odman, D., Werner, E., Dorfman, K.D., Doering, C.R., and B. Mehlig.(2018). Distribution of label spacings for genome mapping in nanochannels. Biomicrofluidics 12, 034115
https://doi.org/10.1063/1.5038417
Reinhart, Wesley F., Reifenberger, Jeff G., Gupta, Damini, Muralidhar, Abhiram, Sheats, Julian, Cao, Han, and Kevin D. Dorfman. (2015). Distribution of distances between DNA barcode labels in nanochannels close to the persistence length. J. Chem. Phys. 142, 064902
https://doi.org/10.1063/1.4907552
E. Werner, G. K. Cheong, D. Gupta, K. D. Dorfman, and B. Mehlig. (2017). One-Parameter Scaling Theory for DNA Extension in a Nanochannel. Phys. Rev. Lett. 119, 268102.
https://doi.org/10.1103/PhysRevLett.119.268102
https://doi.org/10.1063/1.5121305
Odman, D., Werner, E., Dorfman, K.D., Doering, C.R., and B. Mehlig.(2018). Distribution of label spacings for genome mapping in nanochannels. Biomicrofluidics 12, 034115
https://doi.org/10.1063/1.5038417
Reinhart, Wesley F., Reifenberger, Jeff G., Gupta, Damini, Muralidhar, Abhiram, Sheats, Julian, Cao, Han, and Kevin D. Dorfman. (2015). Distribution of distances between DNA barcode labels in nanochannels close to the persistence length. J. Chem. Phys. 142, 064902
https://doi.org/10.1063/1.4907552
E. Werner, G. K. Cheong, D. Gupta, K. D. Dorfman, and B. Mehlig. (2017). One-Parameter Scaling Theory for DNA Extension in a Nanochannel. Phys. Rev. Lett. 119, 268102.
https://doi.org/10.1103/PhysRevLett.119.268102
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National Institutes of Health (Grant No. R01-HG006851)
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Previously Published Citation
Suggested citation
Chuang, Hui-Min; Reifenberger, Jeff G.; Bhandari, Aditya Bikram; Dorfman, Kevin D.. (2019). Data for: Extension distribution for DNA confined in a nanochannel near the Odijk regime. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/99cv-2243.
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