Matching Items (99)
Description
Natural products that target the DNA of cancer cells have been an important source of knowledge and understanding in the development of anticancer chemotherapeutic agents. Bleomycin (BLM) exemplifies this class of DNA damaging agent. The ability of BLM to chelate metal ions and effect oxidative damage of the deoxyribose sugar moiety of DNA has been studied extensively for four decades. Here, the study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal free BLM. The ability of BLM to effect single-stranded was then extensively characterized on both the 3′ and 5′-arms of the hairpin DNAs. The strongly bound DNAs were found to be efficient substrates for Fe·BLM A5-mediated cleavage. Surprisingly, the most prevalent site of damage by BLM was found to be a 5′-AT-3′ dinucleotide sequence. This dinucleotide sequence and others generally not cleaved by BLM when examined using arbitrarily chosen DNA substrate were found in examining the library of ten hairpin DNAs. In total, 111 sites of DNA damage were found to be produced by exposure of the hairpin DNA library to Fe·BLM A5. Also, an assay was developed with which to test the propensity of the hairpin DNAs to undergo double stranded DNA damage. Adapting methods previously described by the Povirk laboratory, one hairpin was characterized using this method. The results were in accordance with those previously reported.
ContributorsSegerman, Zachary (Author) / Hecht, Sidney M. (Thesis advisor) / Levitus, Marcia (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.
ContributorsZhang, Su (Author) / Chaut, John C (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
Single molecules in a tunnel junction can now be interrogated reliably using chemically-functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode ("tethered molecule-pair" configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Importantly, at large tunnel gaps, there exists a regime for many molecules in which the tunneling is influenced more by the chemical identity of the molecules than by variability in the molecule-metal contact. Functionalizing a pair of electrodes with recognition reagents (the "free analyte" configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules.
ContributorsChang, Shuai (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Zhang, Peiming (Committee member) / Tao, Nongjian (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2012
Description
CpG methylation is an essential requirement for the normal development of mammals, but aberrant changes in the methylation can lead to tumor progression and cancer. An in-depth understanding of this phenomenon can provide insights into the mechanism of gene repression. We present a study comparing methylated DNA and normal DNA wrt its persistence length and contour length. Although, previous experiments and studies show no difference between the physical properties of the two, the data collected and interpreted here gives a different picture to the methylation phenomena and its effect on gene silencing. The study was extended to the artificially reconstituted chromatin and its interactions with the methyl CpG binding proteins were also probed.
ContributorsKaur, Parminder (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Tao, Nongjian (Committee member) / Vaiana, Sara (Committee member) / Beckenstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2012
Description
DNA and DNA nanoassemblies such as DNA origamis have large potential in biosensing, drug delivery, nanoelectronic circuits, and biological computing requiring suitable methods for migration and precise positioning. Insulator-based dielectrophoresis (iDEP) provides an efficient and matrix-free approach for manipulation of micro-and nanometer-sized objects. In order to exploit iDEP for naturally formed DNA and DNA nanoassemblies, a detailed understanding of the underlying polarization and dielectrophoretic migration is essential. The shape and the counterion distribution are considered two essential factors in the polarization mechanism. Here, the dielectrophoretic behavior of 6-helix bundle (6HxB) and triangle DNA origamis with identical sequences but substantial topological differences was explored. The polarizability models were discussed for the two species according to their structural difference. The experimental observations reveal distinct iDEP trapping behavior in low frequency AC electric fields in addition to numerical simulations showing a considerable contribution of the electrophoretic transport of the DNA origami species in the DEP trapping regions. Furthermore, the polarizabilities of the two species were determined by measuring the migration times through a potential landscape exhibiting dielectrophoretic barriers. The resulting migration times correlate to the depth of the dielectrophoretic potential barrier and the escape characteristics of the DNA origamis according to an adapted Kramer’s rate model. The orientations of both species in the escape process were studied. Finally, to study the counterion distribution around the DNA molecules, both λ-DNA and 6HxB DNA were used in a phosphate buffer containing magnesium, revealing distinctive negative dielectrophoretic trapping behavior as opposed to positive trapping in a sodium/potassium phosphate buffer system.
ContributorsGan, Lin (Author) / Ros, Alexandra (Thesis advisor) / Buttry, Daniel (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2015
Description
Parkinson’s disease (PD) is a progressive neurodegenerative disorder, diagnosed late in
the disease by a series of motor deficits that manifest over years or decades. It is characterized by degeneration of mid-brain dopaminergic neurons with a high prevalence of dementia associated with the spread of pathology to cortical regions. Patients exhibiting symptoms have already undergone significant neuronal loss without chance for recovery. Analysis of disease specific changes in gene expression directly from human patients can uncover invaluable clues about a still unknown etiology, the potential of which grows exponentially as additional gene regulatory measures are questioned. Epigenetic mechanisms are emerging as important components of neurodegeneration, including PD; the extent to which methylation changes correlate with disease progression has not yet been reported. This collection of work aims to define multiple layers of PD that will work toward developing biomarkers that not only could improve diagnostic accuracy, but also push the boundaries of the disease detection timeline. I examined changes in gene expression, alternative splicing of those gene products, and the regulatory mechanism of DNA methylation in the Parkinson’s disease system, as well as the pathologically related Alzheimer’s disease (AD). I first used RNA sequencing (RNAseq) to evaluate differential gene expression and alternative splicing in the posterior cingulate cortex of patients with PD and PD with dementia (PDD). Next, I performed a longitudinal genome-wide methylation study surveying ~850K CpG methylation sites in whole blood from 189 PD patients and 191 control individuals obtained at both a baseline and at a follow-up visit after 2 years. I also considered how symptom management medications could affect the regulatory mechanism of DNA methylation. In the last chapter of this work, I intersected RNAseq and DNA methylation array datasets from whole blood patient samples for integrated differential analyses of both PD and AD. Changes in gene expression and DNA methylation reveal clear patterns of pathway dysregulation that can be seen across brain and blood, from one study to the next. I present a thorough survey of molecular changes occurring within the idiopathic Parkinson’s disease patient and propose candidate targets for potential molecular biomarkers.
the disease by a series of motor deficits that manifest over years or decades. It is characterized by degeneration of mid-brain dopaminergic neurons with a high prevalence of dementia associated with the spread of pathology to cortical regions. Patients exhibiting symptoms have already undergone significant neuronal loss without chance for recovery. Analysis of disease specific changes in gene expression directly from human patients can uncover invaluable clues about a still unknown etiology, the potential of which grows exponentially as additional gene regulatory measures are questioned. Epigenetic mechanisms are emerging as important components of neurodegeneration, including PD; the extent to which methylation changes correlate with disease progression has not yet been reported. This collection of work aims to define multiple layers of PD that will work toward developing biomarkers that not only could improve diagnostic accuracy, but also push the boundaries of the disease detection timeline. I examined changes in gene expression, alternative splicing of those gene products, and the regulatory mechanism of DNA methylation in the Parkinson’s disease system, as well as the pathologically related Alzheimer’s disease (AD). I first used RNA sequencing (RNAseq) to evaluate differential gene expression and alternative splicing in the posterior cingulate cortex of patients with PD and PD with dementia (PDD). Next, I performed a longitudinal genome-wide methylation study surveying ~850K CpG methylation sites in whole blood from 189 PD patients and 191 control individuals obtained at both a baseline and at a follow-up visit after 2 years. I also considered how symptom management medications could affect the regulatory mechanism of DNA methylation. In the last chapter of this work, I intersected RNAseq and DNA methylation array datasets from whole blood patient samples for integrated differential analyses of both PD and AD. Changes in gene expression and DNA methylation reveal clear patterns of pathway dysregulation that can be seen across brain and blood, from one study to the next. I present a thorough survey of molecular changes occurring within the idiopathic Parkinson’s disease patient and propose candidate targets for potential molecular biomarkers.
ContributorsHenderson, Adrienne Rose (Author) / Huentelman, Matthew J (Thesis advisor) / Newbern, Jason (Thesis advisor) / Dunckley, Travis L (Committee member) / Jensen, Kendall (Committee member) / Wilson, Melissa (Committee member) / Arizona State University (Publisher)
Created2019
Description
Every minute and a half, an American is sexually assaulted (Department of Justice, 2017). After an instance of sexual assault, some victims are given the choice of having a sexual assault evidence kit (SAK) collected. These kits are designed to collect DNA evidence that will, in the best case scenario, result in the identification of the perpetrator. If the perpetrator cannot be located, the DNA profile can still be submitted to the FBI’s CODIS databank, which houses hundreds of thousands of DNA profiles from criminal cases, and may still lead to apprehension of the rapist. Unfortunately, some SAKs experience long delays, decades even, before being tested. To date, there are hundreds of thousands of untested SAKs that remain in police custody awaiting to be submitted for forensic profiling across the country. Here, we completed a holistic investigation of sexual assault response and SAK processing in Arizona. It is important to notice that the focus of our study not only includes SAK processing and the backlog but sexual assault prevention and improving victim reporting in an effort to understand the SAK “pipeline,” from assault to prosecution.
We identified problems in three major categories that negatively impact the SAK pipeline: historical inertia, legislative and institutional limitations, and community awareness. We found that a large number of SAKs in Arizona have remained untested due insufficient funding and staffing for public crime labs making it difficult for state labs to alleviate the SAK backlog while simultaneously responding to incoming cases (“Why the Backlog Exists,” n.d.). However, surveys of ASU undergraduate students revealed a significant interest in campus assault and the SAK backlog. Based on our findings, we suggest harnessing the interest of undergraduate students and recruiting them to specialized SAK-oriented forensic technician and sexual assault nurse examiner (SANE) training at ASU with the goal of creating a workforce that will alleviate the absence of trained professionals within the country. We also explore the possibility of the creation of a private crime laboratory at ASU devoted the processing of SAKs in Arizona as a measure of alleviating the demand on local public laboratories and providing a more economic alternative to commercial laboratories. The creation of an SAK laboratory at ASU would provide undergraduates the opportunity to learn more about real forensic analysis on campus, provide a pipeline for students to become technicians themselves, and help reduce and prevent a future SAK backlog in Arizona.
We identified problems in three major categories that negatively impact the SAK pipeline: historical inertia, legislative and institutional limitations, and community awareness. We found that a large number of SAKs in Arizona have remained untested due insufficient funding and staffing for public crime labs making it difficult for state labs to alleviate the SAK backlog while simultaneously responding to incoming cases (“Why the Backlog Exists,” n.d.). However, surveys of ASU undergraduate students revealed a significant interest in campus assault and the SAK backlog. Based on our findings, we suggest harnessing the interest of undergraduate students and recruiting them to specialized SAK-oriented forensic technician and sexual assault nurse examiner (SANE) training at ASU with the goal of creating a workforce that will alleviate the absence of trained professionals within the country. We also explore the possibility of the creation of a private crime laboratory at ASU devoted the processing of SAKs in Arizona as a measure of alleviating the demand on local public laboratories and providing a more economic alternative to commercial laboratories. The creation of an SAK laboratory at ASU would provide undergraduates the opportunity to learn more about real forensic analysis on campus, provide a pipeline for students to become technicians themselves, and help reduce and prevent a future SAK backlog in Arizona.
ContributorsStewart, Jamie (Co-author) / Brokaw, Danielle (Co-author) / Stone, Megan (Co-author) / Kanthaswamy, Sreetharan (Thesis director) / Oldt, Robert (Committee member) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The effects that forensic-themed programs such as CSI: Crime Scene Investigation has on the public's understanding and expectations of the criminal justice system has been a main focus of study in recent years. This phenomenon was coined by the media and termed the "CSI Effect." This study aimed to research the correlations between age, gender, and program-watching habits on potential juries' evidence expectations in court. To do so, 70 people were surveyed and asked a series of demographic questions, as well as questions about how often they watch forensic-themed shows and their experience with the criminal justice system. They were given a mock crime scene scenario and asked about their scientific and non-scientific evidence expectations in this particular case. The most notable results showed that a longer exposure time to forensic-themed programs correlated to high evidence expectations. However, how often viewers watch forensic-themed programs did not seem to affect their evidence expectations. It was concluded that the higher evidence expectations by modern jurors may be due to a combination of the "CSI Effect" and the newly hypothesized "Tech Effect," instead of just being the consequence of the watching too much forensic-themed television.
ContributorsJones, Kristin Taylor (Author) / Kobojek, Kimberly (Thesis director) / Lafond, Sue (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2014-05
Description
Abstract Molecular Engineering of Novel Polymeric Agents for Targeted Cancer Gene Therapy Dana Matthews Cancer gene cell therapy is a strategy that involves the administration of genes for correcting the effect of mutated cancer cells in order to induce tumor cell death. In particular, genes that encode for pro-apoptotic proteins can result in death of tumor cells. Prostate cancer is a very common cancer among males in America, and as highly destructive chemotherapy and radiation are generally the only treatments available once the cancer has metastasized, there is a need for the development of treatments that can specifically target and kill prostate cancer cells, while demonstrating low toxicity to other tissue. This experiment will attempt to create such a treatment through gene therapy techniques. The parallel synthesis and DNA binding affinity assay utilized in these experiments have produced a polymer that surpasses pEI-25, a gene delivery polymer standard, in both transfection efficacy and low cytotoxicity and trafficking of polyplexes in the cell, and finding methods to increase the transfection efficacy and specificity of polyplexes for PC3-PSMA cells.
ContributorsMatthews, Dana (Author) / Rege, Kaushal (Thesis director) / Linton, Rebecca (Committee member) / Huang, Huang-Chial (Committee member) / Barrett, The Honors College (Contributor)
Created2008-12
Description
Photophysical Studies of the DNA Microenvironment and Small Molecule-DNA Interactions
The photophysical properties of ethidium in a variety of organic solvents, as well as several dsDNAs, were measured. We report that the fluorescence quantum yield of intercalated ethidium is .30(.03), which falls between previous stated measurements of .14 and .60. We believe this to be the most accurately measured fluorescence quantum yield to date, as verified by Strickler-Berg analyses, which exhibit excellent agreement with experimental fluorescence lifetimes. A marked hypochromism upon binding to DNA is noted due to interactions of the dye’s and nucleobases’ respective π-stacks. This more than counteracts the expected increase in transition dipole due to increased conjugation caused by twisting of the phenyl moiety upon intercalation.
The reduced volume cylinder model was tested by the quenching of the fluorescence of an intercalator (ethidium bromide) by a groove binder (methyl viologen). We report that the model is not accurate over a relevant range of DNA concentrations.
The photophysical properties of ethidium in a variety of organic solvents, as well as several dsDNAs, were measured. We report that the fluorescence quantum yield of intercalated ethidium is .30(.03), which falls between previous stated measurements of .14 and .60. We believe this to be the most accurately measured fluorescence quantum yield to date, as verified by Strickler-Berg analyses, which exhibit excellent agreement with experimental fluorescence lifetimes. A marked hypochromism upon binding to DNA is noted due to interactions of the dye’s and nucleobases’ respective π-stacks. This more than counteracts the expected increase in transition dipole due to increased conjugation caused by twisting of the phenyl moiety upon intercalation.
The reduced volume cylinder model was tested by the quenching of the fluorescence of an intercalator (ethidium bromide) by a groove binder (methyl viologen). We report that the model is not accurate over a relevant range of DNA concentrations.
ContributorsEngelhart, Aaron (Author) / Gould, Ian (Thesis director) / Francisco, Wilson (Committee member) / Bednar, Valerie (Committee member) / Barrett, The Honors College (Contributor)
Created2005-05