Browsing by Author "Cao, Han"
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Item Data from: Distribution of distances between DNA barcode labels in nanochannels close to the persistence length(2015-02-14) Reinhart, Wesley F; Reifenberger, Jeff G.; Gupta, Damini; Muralidhar, Abhiram; Sheats, Julian; Cao, Han; Dorfman, Kevin D.Item Data from: Measurements of DNA barcode label separations in nanochannels from time-series data(2015) Sheats, Julian; Reifenberger, Jeff G.; Cao, Han; Dorfman, Kevin D.Item Data from: Measuring the wall depletion length of nanoconfined DNA (2018)(2018-09-20) Bhandari, Aditya B; Reifenberger, Jeffrey G; Chuang, Hui-Min; Cao, Han; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; DorfmanEfforts to study the polymer physics of DNA con ned in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and nite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 m (88,325 base pairs) between nick pairs. In excess of 5 million measurements of the fractional extension were obtained from 39,291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly con ned wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fi t to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.Item Data from: Modeling the relaxation of internal DNA segments during genome mapping in nanochannels(2016) Jain, Aashish; Sheats, Julian; Reifenberger, Jeffery G; Cao, Han; Dorfman, Kevin DItem Data from: Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel(2018) Reifenberger, Jeffrey G; Cao, Han; Dorfman, Kevin DItem Data from: Sequence-Dependent Persistence Length of Long DNA(2017-12-05) Chuang, Hui-Min; Reifenberger, Jeffrey G; Cao, Han; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin DUsing a high-throughput genome-mapping approach, we obtained circa 50 million measurements of the extension of internal human DNA segments in a 41 nm × 41 nm nanochannel. The underlying DNA sequences, obtained by mapping to the reference human genome, are 2.5–393 kilobase pairs long and contain percent GC contents between 32.5% and 60%. Using Odijk’s theory for a channel-confined wormlike chain, these data reveal that the DNA persistence length increases by almost 20% as the percent GC content increases. The increased persistence length is rationalized by a model, containing no adjustable parameters, that treats the DNA as a statistical terpolymer with a sequence-dependent intrinsic persistence length and a sequence-independent electrostatic persistence length.Item Data from: Topological events in single molecules of E. coli DNA confined in nanochannels(2015) Reifenberger, Jeff G.; Dorfman, Kevin D.; Cao, HanItem A simple model for the wall depletion length of nanoconfined DNA (preprint)(2018-05-17) Bhandari, Aditya Bikram; Reifenberger, Jeffrey G; Chuang, Hui-Min; Cao, Han; Dorfman, Kevin D