Browsing by Author "Chuang, Hui-Min"

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    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 Lab
    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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    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; Dorfman
    Efforts 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.
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    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 D
    Using 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.
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    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
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    Study of DNA Physics by a High-Throughput Genome Mapping Technique
    (2019-09) Chuang, Hui-Min
    Next generation sequencing (NGS) is a powerful tool to sequence DNA with a low error rate at an affordable cost. While NGS is successful with these features, its short-read length leads to difficulty in detecting structural variation of chromosome at a large scale. Labeling barcodes can help resolve these drawbacks by generating scaffolds and can detect structural variation in combination with NGS. Though the labeling barcode technique is well-developed experimentally, how interpreting the data correctly still needs improvement. The properties and behavior of DNA in confinement are not fully understood and thus there is disagreement between experiments and theory. The aim of this dissertation research is to improve data interpretation by correcting assumptions which were misused or even not considered in previous studies. Using a high-throughput genome mapping technique, we first found a strong correlation between the persistence length of long DNA and sequence composition, which was oversimplified in previous works. We developed a statistical terpolymer model to rationalize the experimental results. We next revisited a widely used DNA model, a neutral wormlike chain model, through a comparison of experimental data sets with theory. We did a dimensional analysis and proposed that DNA-wall electrostatic interactions, which were neglected in the model, are the cause for the disagreement between experiments and theory. We hope all the findings in this dissertation provide a deeper understanding of properties and behavior of DNA in confinement and inspire scientists toward a new research direction to make a more robust DNA model for data interpretation of DNA-based experiments.