Browsing by Subject "Nanochannels"

Now showing 1 - 3 of 3
  • Thumbnail Image
    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; 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.
  • Thumbnail Image
    Item
    Equilibrium properties of DNA and other semiflexible polymers confined in nanochannels
    (2016-01) Muralidhar, Abhiram
    Recent developments in next-generation sequencing (NGS) techniques have opened the door for low-cost, high-throughput sequencing of genomes. However, these developments have also exposed the inability of NGS to track large scale genomic information, which are extremely important to understand the relationship between genotype and phenotype. Genome mapping offers a reliable way to obtain information about large-scale structural variations in a given genome. A promising variant of genome mapping involves confining single DNA molecules in nanochannels whose cross-sectional dimensions are approximately 50 nm. Despite the development and commercialization of nanochannel-based genome mapping technology, the polymer physics of DNA in confinement is only beginning to be understood. Apart from its biological relevance, DNA is also used as a model polymer in experiments by polymer physicists. Indeed, the seminal experiments by Reisner et al. (2005) of DNA confined in nanochannels of different widths revealed discrepancies with the classical theories of Odijk and de Gennes for polymer confinement. Picking up from the conclusions of the dissertation of Tree (2014), this dissertation addresses a number of key outstanding problems in the area of nanoconfined DNA. Adopting a Monte Carlo chain growth technique known as the pruned-enriched Rosenbluth method, we examine the equilibrium and near-equilibrium properties of DNA and other semiflexible polymers in nanochannel confinement. We begin by analyzing the dependence of molecular weight on various thermodynamic properties of confined semiflexible polymers. This allows us to point out the finite size effects that can occur when using low molecular weight DNA in experiments. We then analyze the statistics of backfolding and hairpin formation in the context of existing theories and discuss how our results can be used to engineer better conditions for genome mapping. Finally, we elucidate the diffusion behavior of confined semiflexible polymers by comparing and contrasting our results for asymptotically long chains with other similar studies in the literature. We expect our findings to be not only beneficial to the design of better genome mapping devices, but also to the fundamental understanding of semiflexible polymers in confinement.
  • Thumbnail Image
    Item
    Static and Dynamic Properties of DNA Confined in Nanochannels
    (2017-10) Gupta, Damini
    Next-generation sequencing (NGS) techniques have considerably reduced the cost of high-throughput DNA sequencing. However, it is challenging to detect large-scale genomic variations by NGS due to short read lengths. Genome mapping can easily detect large-scale structural variations because it operates on extremely large intact molecules of DNA with adequate resolution. One of the promising methods of genome mapping is based on confining large DNA molecules inside a nanochannel whose cross-sectional dimensions are approximately 50 nm. Even though this genome mapping technology has been commercialized, the current understanding of the polymer physics of DNA in nanochannel confinement is based on theories and lacks much needed experimental support. The results of this dissertation are aimed at providing a detailed experimental understanding of equilibrium properties of nanochannel-confined DNA molecules. The results are divided into three parts. In first part, we evaluate the role of channel shape on thermodynamic properties of channel confined DNA molecules using a combination of fluorescence microscopy and simulations. Specifically, we show that high aspect ratio of rectangular channels significantly alters the chain statistics as compared to an equivalent square channel with same cross-sectional area. In the second part, we present experimental evidence that weak excluded volume effects arise in DNA nanochannel confinement, which form the physical basis for the extended de Gennes regime. We also show how confinement spectroscopy and simulations can be combined to reduce molecular weight dispersity effects arising from shearing, photo-cleavage, and nonuniform staining of DNA. Finally, the third part of the thesis concerns the dynamic properties of nanochannel confined DNA. We directly measure the center-of-mass diffusivity of single DNA molecules in confinement and show that that it is necessary to modify the classical results of de Gennes to account for local chain stiffness of DNA in order to explain the experimental results. In the end, we believe that our findings from the experimental test of the phase diagram for channel-confined DNA, with careful control over molecular weight dispersity, channel geometry, and electrostatic interactions, will provide a firm foundation for the emerging genome mapping technology.