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Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges

Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.
ContributorsLiu, Hao (Author) / Lindsay, Stuart M (Committee member) / Yan, Hao (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2013
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In eukaryotes, DNA is packed in a highly condensed and hierarchically organized structure called chromatin, in which DNA tightly wraps around the histone octamer consisting of one histone 3-histone 4 (H3-H4) tetramer and two histone 2A- histone 2B (H2A-H2B) dimers with 147 base pairs in an almost two left handed

In eukaryotes, DNA is packed in a highly condensed and hierarchically organized structure called chromatin, in which DNA tightly wraps around the histone octamer consisting of one histone 3-histone 4 (H3-H4) tetramer and two histone 2A- histone 2B (H2A-H2B) dimers with 147 base pairs in an almost two left handed turns. Almost all DNA dependent cellular processes, such as DNA duplication, transcription, DNA repair and recombination, take place in the chromatin form. Based on the critical importance of appropriate chromatin condensation, this thesis focused on the folding behavior of the nucleosome array reconstituted using different templates with various controllable factors such as histone tail modification, linker DNA length, and DNA binding proteins. Firstly, the folding behaviors of wild type (WT) and nucleosome arrays reconstituted with acetylation on the histone H4 at lysine 16 (H4K16 (Ac)) were studied. In contrast to the sedimentation result, atomic force microscopy (AFM) measurements revealed no apparent difference in the compact nucleosome arrays between WT and H4K16 (Ac) and WT. Instead, an optimal loading of nucleosome along the template was found necessary for the Mg2+ induced nucleosome array compaction. This finding leads to the further study on the role of linker DNA in the nucleosome compaction. A method of constructing DNA templates with varied linker DNA lengths was developed, and uniformly and randomly spaced nucleosome arrays with average linker DNA lengths of 30 bp and 60 bp were constructed. After comprehensive analyses of the nucleosome arrays' structure in mica surface, the lengths of the linker DNA were found playing an important role in controlling the structural geometries of nucleosome arrays in both their extended and compact forms. In addition, higher concentration of the DNA binding domain of the telomere repeat factor 2 (TRF2) was found to stimulate the compaction of the telomeric nucleosome array. Finally, AFM was successfully applied to investigate the nucleosome positioning behaviors on the Mouse Mammary Tumor Virus (MMTV) promoter region, and two highly positioned region corresponded to nucleosome A and B were identified by this method.
ContributorsFu, Qiang (Author) / Lindsay, Stuart M (Thesis advisor) / Yan, Hao (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2010
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Franklin William Stahl studied DNA replication, bacteriophages, and genetic recombination in the US during the mid-twentieth and early twenty-first centuries. With his colleague Matthew Meselson, Stahl performed an experiment called the Meselson-Stahl experiment, which provided evidence for a process called semi-conservative DNA replication. Semi-conservative replication is a process in which

Franklin William Stahl studied DNA replication, bacteriophages, and genetic recombination in the US during the mid-twentieth and early twenty-first centuries. With his colleague Matthew Meselson, Stahl performed an experiment called the Meselson-Stahl experiment, which provided evidence for a process called semi-conservative DNA replication. Semi-conservative replication is a process in which each strand of a parental DNA double helix serves as a template for newly replicated daughter strands, so that one parental strand is conserved in every daughter double helix. Those findings supported the Watson-Crick Model for DNA replication proposed in 1953 by James Watson and Francis Crick, convincing many biologists about DNA’s structure and replication in the 1950s. Stahl’s genetics research, especially that of DNA replication, showed researchers how genetic information is distributed within a cell and is passed down from cell to cell.

Created2017-07-20
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On 6 May 1952, at King’s College London in London, England, Rosalind Franklin photographed her fifty-first X-ray diffraction pattern of deoxyribosenucleic acid, or DNA. Photograph 51, or Photo 51, revealed information about DNA’s three-dimensional structure by displaying the way a beam of X-rays scattered off a pure fiber of DNA.

On 6 May 1952, at King’s College London in London, England, Rosalind Franklin photographed her fifty-first X-ray diffraction pattern of deoxyribosenucleic acid, or DNA. Photograph 51, or Photo 51, revealed information about DNA’s three-dimensional structure by displaying the way a beam of X-rays scattered off a pure fiber of DNA. Franklin took Photo 51 after scientists confirmed that DNA contained genes. Maurice Wilkins, Franklin’s colleague showed James and Francis Crick Photo 51 without Franklin’s knowledge. Watson and Crick used that image to develop their structural model of DNA. In 1962, after Franklin’s death, Watson, Crick, and Wilkins shared the Nobel Prize in Physiology or Medicine for their findings about DNA. Franklin’s Photo 51 helped scientists learn more about the three-dimensional structure of DNA and enabled scientists to understand DNA’s role in heredity.

Created2019-12-30
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In May 1953, scientists James Watson and Francis Crick wrote the article “Genetical Implications of the Structure of Deoxyribonucleic Acid,” hereafter “Genetical Implications,” which was published in the journal Nature. In “Genetical Implications,” Watson and Crick suggest a possible explanation for deoxyribonucleic acid, or DNA, replication based on a structure

In May 1953, scientists James Watson and Francis Crick wrote the article “Genetical Implications of the Structure of Deoxyribonucleic Acid,” hereafter “Genetical Implications,” which was published in the journal Nature. In “Genetical Implications,” Watson and Crick suggest a possible explanation for deoxyribonucleic acid, or DNA, replication based on a structure of DNA they proposed prior to writing “Genetical Implications.” Watson and Crick proposed their theory about DNA replication at a time when scientists had recently reached the consensus that DNA contained genes, which scientists understood to carry information that determines an organism’s identity. Watson and Crick’s replication mechanism as presented in “Genetical Implications” contributed to the two scientists sharing a portion of the 1962 Nobel Prize in Physiology or Medicine. With their suggested DNA replication mechanism in “Genetical Implications,” Watson and Crick explained how genes are copied and passed along to new cells and organisms, thereby explaining how the information contained within genes is preserved through generations.

Created2020-01-13
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In April 1953, Rosalind Franklin and Raymond Gosling, published “Molecular Configuration in Sodium Thymonucleate,” in the scientific journal Nature. The article contained Franklin and Gosling’s analysis of their X-ray diffraction pattern of thymonucleate or deoxyribonucleic acid, known as DNA. In the early 1950s, scientists confirmed that genes, the heritable factors

In April 1953, Rosalind Franklin and Raymond Gosling, published “Molecular Configuration in Sodium Thymonucleate,” in the scientific journal Nature. The article contained Franklin and Gosling’s analysis of their X-ray diffraction pattern of thymonucleate or deoxyribonucleic acid, known as DNA. In the early 1950s, scientists confirmed that genes, the heritable factors that control how organisms develop, contained DNA. However, at the time scientists had not determined how DNA functioned or its three-dimensional structure. In their 1953 paper, Franklin and Gosling interpret X-ray diffraction patterns of DNA fibers that they collected, which show the scattering of X-rays from the fibers. The patterns provided information about the three-dimensional structure of the molecule. “Molecular Configuration in Sodium Thymonucleate” shows the progress Franklin and Gosling made toward understanding the three-dimensional structure of DNA.

Created2019-11-30
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In 2001, Yale University Press published Frederic Lawrence Holmes' book, Meselson, Stahl, and the Replication of DNA: A History of "The Most Beautiful Experiment in Biology" (Replication of DNA), which chronicles the 1950s debate about how DNA replicates. That experiment verified that DNA replicates semi-conservatively as originally proposed by Watson

In 2001, Yale University Press published Frederic Lawrence Holmes' book, Meselson, Stahl, and the Replication of DNA: A History of "The Most Beautiful Experiment in Biology" (Replication of DNA), which chronicles the 1950s debate about how DNA replicates. That experiment verified that DNA replicates semi-conservatively as originally proposed by Watson and Crick. Rather than focusing solely on experiments and findings, Holmes's book presents the investigative processes of scientists studying DNA replication. Based on personal accounts, letter correspondence, and preserved research documents, Replication of DNA serves as a detailed account of the initial issues surrounding DNA replication and the Meselson-Stahl experiment from a scientist's perspective.

Created2017-07-23
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In February 1953, Linus Pauling and Robert Brainard Corey, two scientists working at the California Institute of Technology in Pasadena, California, proposed a structure for deoxyribonucleic acid, or DNA, in their article “A Proposed Structure for the Nucleic Acids,” henceforth “Nucleic Acids.” In the article, Pauling and Corey suggest a

In February 1953, Linus Pauling and Robert Brainard Corey, two scientists working at the California Institute of Technology in Pasadena, California, proposed a structure for deoxyribonucleic acid, or DNA, in their article “A Proposed Structure for the Nucleic Acids,” henceforth “Nucleic Acids.” In the article, Pauling and Corey suggest a model for nucleic acids, including DNA, that consisted of three nucleic acid strands wound together in a triple helix. “Nucleic Acids” was published in Proceedings of the National Academy of Sciences shortly after scientists came to the consensus that genes, the biological factors that control how organisms develop, contained DNA. Though scientists proved Pauling and Corey’s model incorrect, “Nucleic Acids” helped scientists understand DNA’s structure and function as genetic material.

Created2019-08-26
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In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty published an article in which they concluded that genes, or molecules that dictate how organisms develop, are made of deoxyribonucleic acid, or DNA. The article is titled “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction

In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty published an article in which they concluded that genes, or molecules that dictate how organisms develop, are made of deoxyribonucleic acid, or DNA. The article is titled “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III,” hereafter “Transformation.” The authors isolated, purified, and characterized genes within bacteria and found evidence that those genes were made of DNA and not protein. Though scientists were initially skeptical that genes were made of DNA, they later recognized that the data reported in “Transformation” were clear evidence that DNA was genetic material, a revelation that furthered research about how organisms grow, develop, and pass on traits to offspring.

Created2019-07-08
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In 1951 and 1952, Alfred Hershey and Martha Chase conducted a series of experiments at the Carnegie Institute of Washington in Cold Spring Harbor, New York, that verified genes were made of deoxyribonucleic acid, or DNA. Hershey and Chase performed their experiments, later named the Hershey-Chase experiments, on viruses that

In 1951 and 1952, Alfred Hershey and Martha Chase conducted a series of experiments at the Carnegie Institute of Washington in Cold Spring Harbor, New York, that verified genes were made of deoxyribonucleic acid, or DNA. Hershey and Chase performed their experiments, later named the Hershey-Chase experiments, on viruses that infect bacteria, also called bacteriophages. The experiments followed decades of scientists’ skepticism about whether genetic material was composed of protein or DNA. The most well-known Hershey-Chase experiment, called the Waring Blender experiment, provided concrete evidence that genes were made of DNA. The Hershey-Chase experiments settled the long-standing debate about the composition of genes, thereby allowing scientists to investigate the molecular mechanisms by which genes function in organisms.

Created2019-06-23