Browsing by Subject "Genome mapping"

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    Bridging the gap between theory, experiments and simulations of nanochannel confined DNA
    (2020-08) Bhandari, Aditya Bikram
    The study of nanochannel confined DNA has garnered substantial attention since the early 2000's owing to its application in genome mapping, the coarse-grained counterpart to DNA sequencing, which is an indispensable tool in biological research. However, our understanding of the physics behind confined DNA is rather simplified and incomplete. Thus, theory, simulation and experiment have by and large been at odds with one another. The results of this dissertation are aimed at understanding and attempting to resolve the source of these discrepancies. Our strategy for this dissertation is three-pronged. First, we revisit a historically cited explanation for the discrepancies - the lack of understanding behind the wall depletion length denoting the wall-DNA electrostatic interactions. Second, we considered the intersection of theory and simulation, which recent developments have managed to bring sufficiently into accord. We found that the deviations between the fractional extension distributions predicted by an asymptotic theory and those observed experimentally, are not due to a breakdown of the theory, even for experimental conditions which typically do not strictly satisfy the asymptotic limits of the theory. This motivated a closer inspection of the theories to determine a missing link between theory and experiment. Finally, by studying a recently generated dataset of fractional extensions spanning a wide range of the experimental parameter space, we were able to isolate this missing link as the effect of long-range electrostatics in the system which are typically ignored in the simplified theories, wherein the DNA is assumed as a neutral polymer confined in a channel of a reduced effective channel size. We believe that our findings within this dissertation will provide a better understanding of confined polymers and, in particular, the nanochannel confined DNA system used in genome mapping, as well as provide new directions of study in the future.
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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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    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.