Browsing by Author "University of Minnesota Dorfman Research Lab"
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Item Data for "Microfluidic long DNA sample preparation from cells" published as Lab Chip, 2019, 19, 281(2019-01-18) Agrawal, Paridhi; Dorfman, Kevin; agraw135@umn.edu; Agrawal, Paridhi; University of Minnesota Dorfman Research LabThis is the data for the article published as "Microfluidic long DNA sample preparation from cells" in Lab on a chip. The data includes DNA molecular weight distribution analysis and DNA concentration measurements from fluorometry data.Item Data for DNA fragmentation in a steady shear flow(2022-09-23) Qiao, Yiming; Ma, Zixue; Onyango, Clive; Cheng, Xiang; Dorfman, Kevin D; qiao0017@umn.edu; Qiao, Yiming; University of Minnesota Dorfman Research LabWe have determined the susceptibility of T4 DNA (166 kilobase pairs, kbp) to fragmentation under steady shear in a cone-and-plate rheometer.Item Data for: Diffusion of Knots along DNA Confined in Nanochannels(2020-08-05) Ma, Zixue; Dorfman, Kevin D; ma000052@umn.edu; Ma, Zixue; University of Minnesota Dorfman Research LabWe study the diffusion of knots along relaxed DNA in nanochanels using a nanofluidic "knot factory" device for knot generation. The knot diffusion data for the article is published as "Diffusion of knots along DNA Confined in Nanochannels" in Macromolecules. The data includes DNA images before and after knot generation and all the data used to generate the figures in the article.Item Data for: Diffusion of knotted DNA molecules in nanochannels in the extended de Gennes regime(2021-04-19) Ma, Zixue; Dorfman, Kevin D; ma000052@umn.edu; Ma, Zixue; University of Minnesota Dorfman Research LabWe study the effect of knots on DNA diffusion in nanochannels using a nanofluidic "knot factory" device for knot generation. The unknotted and knotted DNA diffusion data for the article is published as "Diffusion of knotted DNA molecules in nanochannels in the extended de Gennes regime" in Macromolecules. The data includes DNA images before and after knot generation and all the data used to generate the figures in the article.Item Data for: Extension distribution for DNA confined in a nanochannel near the Odijk regime(2019-09-19) Chuang, Hui-Min; Reifenberger, Jeff G.; Bhandari, Aditya Bikram; Dorfman, Kevin D.; dorfman@umn.edu; Dorfman, Kevin D.; University of Minnesota Dorfman Research LabDNA 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.Item V2 Data for: Interactions between two knots in nanochannel-confined DNA molecules(2021-08-14) Ma, Zixue; Dorfman, Kevin D; ma000052@umn.edu; Ma, Zixue; University of Minnesota Dorfman Research LabWe study the interaction between knots in nanochannel-confined DNA molecules using a nanofluidic "knot factory" device for knot generation. The two-knot interaction data for the article is published as "Interactions between two knots in nanochannel-confined DNA molecules" in Journal of Chemical Physics. The data includes DNA images after two-knot generation and all the data used to generate the figures in the article.