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DNA

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Articles 1 - 30 of 86

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Co-Option Of The Gibbon-Specific Lava Retrotransposon In Dna Repair Pathways, Mariam Okhovat, Kimberly A. Nevonen, Brett Davis, Pryce S. Michener, Samantha Ward, Mark Milhaven, Lana Harshman, Ajuni Sohota, Rachel J. O’Neill, Nadav Ahituv, Krishna R. Veeramah, Lucia Carbone Sep 2019

Co-Option Of The Gibbon-Specific Lava Retrotransposon In Dna Repair Pathways, Mariam Okhovat, Kimberly A. Nevonen, Brett Davis, Pryce S. Michener, Samantha Ward, Mark Milhaven, Lana Harshman, Ajuni Sohota, Rachel J. O’Neill, Nadav Ahituv, Krishna R. Veeramah, Lucia Carbone

University of Massachusetts Medical School Faculty Publications

Transposable elements (TEs) can shape gene regulation networks by being co-opted as enhancers. However, the contribution of lineage-specific TE insertions to recent adaptations remains poorly understood. Gibbons present a suitable model to study these contributions, as they have evolved many distinct traits, including heavily rearranged genomes and a novel TE called LAVA. The LAVA retrotransposon is still active in the gibbon genome and is thought to have contributed to evolution of gibbon-specific traits. In this study, we characterized fixed and polymorphic LAVA insertions across multiple gibbon genomes and found that 10% of all LAVA elements overlap chromatin states associated with ...


Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic May 2019

Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic

Faculty Publications

The DNA molecule can be modeled as a quantum logic processor in which electron spin qubits are held coherently in each nucleotide in a logically and thermodynamically reversible enantiomeric symmetry, and can be coherently conducted along the pi-stacking interactions of aromatic nucleotide bases, while simultaneously being spin-filtered via the helicity of the DNA molecule. Entangled electron pairs can be separated by that spin-filtering, held coherently at biological temperatures in the topologically insulated nucleotide quantum gates, and incorporated into separate DNA strands during DNA replication. Two separate DNA strands that share quantum entangled electrons can be mitotically divided into individual cells ...


Toward A Rhetoric Of Dna: The Advent Of Crispr, Michael J. Zerbe Feb 2019

Toward A Rhetoric Of Dna: The Advent Of Crispr, Michael J. Zerbe

Poroi

The nucleic acid DNA, which contains an organism’s genetic information, consists of a four-letter alphabet that has until recently been characterized as a read-only text. The development of a quick, inexpensive DNA targeting and manipulation technique called CRISPR, pronounced “crisper,” though, has changed DNA from this arhetorical, read-only data set, as it has been characterized in the rhetoric literature to date, to a fully rhetorical text—one that can be not only read but created, interpreted, copied, altered, and stored as well. The Book of Nature, an idea with roots in antiquity but popularized during the nineteenth century, provides ...


Unintended Consequences Of Dna Analysis Delays In North Carolina, Pamela Cook Woodard Jan 2019

Unintended Consequences Of Dna Analysis Delays In North Carolina, Pamela Cook Woodard

Walden Dissertations and Doctoral Studies

The processing of DNA recovered from felony crime scenes often causes delays in trials of up to 3 years, calling into question defendants' rights to a speedy trial. Using Lewin's force field analysis as the theoretical framework, the purpose of this quantitative, comparative study was to compare the processing and reporting of results related to DNA testing in 4 states. Survey data were collected from state bar members (n=137), members of a professional law organization (n=149), and members of a state DNA laboratory (n=20). The purpose of this quantitative, comparative study was to determine whether these ...


Student Understanding Of Dna Structure–Function Relationships Improves From Using 3d Learning Modules With Dynamic 3d Printed Models, Michelle E. Howell, Christine S. Booth, Sharmin M. Sikich, Tomáš Helikar, Rebecca Roston, Brain A. Couch, Karin Van Dijk Jan 2019

Student Understanding Of Dna Structure–Function Relationships Improves From Using 3d Learning Modules With Dynamic 3d Printed Models, Michelle E. Howell, Christine S. Booth, Sharmin M. Sikich, Tomáš Helikar, Rebecca Roston, Brain A. Couch, Karin Van Dijk

Biochemistry -- Faculty Publications

Understanding the relationship between molecular structure and function represents an important goal of undergraduate life sciences. Although evidence suggests that handling physical models supports gains in student understanding of structure–function relationships, such models have not been widely implemented in biochemistry classrooms. Three-dimensional (3D) printing represents an emerging cost-effective means of producing molecular models to help students investigate structure–function concepts. We developed three interactive learning modules with dynamic 3D printed models to help biochemistry students visualize biomolecular structures and address particular misconceptions. These modules targeted specific learning objectives related to DNA and RNA structure, transcription factor-DNA interactions, and DNA ...


An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald Apr 2018

An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald

University of Massachusetts Medical School Faculty Publications

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. We benchmarked the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We also used the pipeline to extend our understanding of TtAgo by measuring the protein's binding kinetics at ...


Thermodynamics In Large Hairpin Polyamide-Dna Interactions, Yang Song Mar 2018

Thermodynamics In Large Hairpin Polyamide-Dna Interactions, Yang Song

Dissertations

Human papillomavirus (HPV) is a common sexually transmitted virus responsible for cervical cancers, and its infection is currently incurable. Only a few vaccines against high-risk HPV strains are available. Hairpin polyamides (PAs) in different sizes (8-20 units long) bind DNA in different lengths. They have been shown to have different anti-HPV activities in cell culture.

The interaction between PA and DNA is stabilized by two types of molecular forces: attractive and repulsive forces. Attractive forces include hydrogen bonds, van der Waals contacts and electrostatic forces between PA and DNA. Repulsive forces include the hydrophobic effect, which forces the PA out ...


A Novel Method To Analyze Dna Breaks And Repair In Human Cells, Caitlin Elizabeth Goodman Jan 2018

A Novel Method To Analyze Dna Breaks And Repair In Human Cells, Caitlin Elizabeth Goodman

Browse all Theses and Dissertations

Microsatellites repeat sequences are prone to forming non-canonical DNA structures and mutations. These areas of the genome can undergo expansions and contractions and are responsible for a variety of inherited neurological and neuromuscular disorders. Hairpin structures formed by trinucleotide repeats can lead to replication fork stalling, and fork collapse causing DNA double strand breaks. Various mechanisms are involved in processing microsatellites including mismatch repair, base excision repair, and crossover junction endonuclease cleavage. These processes, which are supposed to protect the genome, could also be the culprits which are causing mutations. In order to test and study this hypothesis, the use ...


Liquid Crystal Phases Of Rna Mononucleosides, Emily Hayden Jan 2018

Liquid Crystal Phases Of Rna Mononucleosides, Emily Hayden

Undergraduate Honors Theses

Deoxyribonucleic Acid (DNA) can form columnar liquid crystal phases in solutions of both short strand, base-pair oligomer solutions, and in solutions of single DNA Nucleoside Tri-Phosphates (dNTP), the molecular constituents that make up helical DNA. The spontaneous phase transition to columnar liquid crystals by the dNTPs occurs without the necessity of the sugar-phosphate backbone of helical DNA, and exhibits key structural elements of biologic nucleic acids including long-range columnar stacking of base-pairs and Watson-Crick selectivity. This spontaneous increase in structural complexity is useful when discussing liquid crystal formation as relevant to the increasingly complexity of prebiotic life.

Ribonucleic acid (RNA ...


Potential Synthesis Pathway For Redox-Active Dna Nucleoside, Nicole Broda Jan 2018

Potential Synthesis Pathway For Redox-Active Dna Nucleoside, Nicole Broda

Undergraduate Honors Theses

Science has failed those who die from the treatment of an illness rather than the illness itself. DNA nanomachines hold the promise of improving the site specificity of drug delivery, which can combat the toxicity of the drug to healthy cells and in turn, decrease unnecessary patient deaths due to treatment. We have found a novel synthesis pathway for a reversible redox- active nucleoside (n-nucleoside) that has the promise to be incorporated in and create redox- active DNA. Synthesis of 5’-deazalloxazine-ribonolactone was achieved via sodium hydride catalyzed glycosylation of 1-a-chloro-3,5-ditoluoyl-2-deoxy-D-ribose (5’,3’-protected-chloro- ribose). We were not able ...


The Study Of Tissue-Specific Dna Methylation As A Method For The Epigenetic Discrimination Of Forensic Samples, Joana Ap Antunes Nov 2017

The Study Of Tissue-Specific Dna Methylation As A Method For The Epigenetic Discrimination Of Forensic Samples, Joana Ap Antunes

FIU Electronic Theses and Dissertations

In forensic sciences, the serological methods used to determine which body fluid was collected from the crime scene are merely presumptive or labor intensive since they rely on protein detection or on microscopic identification of cells. Given that certain forensic cases may need the precise identification of a body fluid to determine criminal contact, such is the example of a suspected sexual assault of a minor; certainty in the body fluid of origin may depict a precise picture of the events. The identification of loci that show differences in methylation according to the tissue of origin can aid forensic analysts ...


Quaternary Interactions And Supercoiling Modulate The Cooperative Dna Binding Of Agt, Manana Melikishvili, Michael G. Fried Jul 2017

Quaternary Interactions And Supercoiling Modulate The Cooperative Dna Binding Of Agt, Manana Melikishvili, Michael G. Fried

Center for Structural Biology Faculty Publications

Human O6-alkylguanine-DNA alkyltransferase (AGT) repairs mutagenic O6-alkylguanine and O4-alkylthymine adducts in single-stranded and duplex DNAs. The search for these lesions, through a vast excess of competing, unmodified genomic DNA, is a mechanistic challenge that may limit the repair rate in vivo. Here, we examine influences of DNA secondary structure and twist on protein–protein interactions in cooperative AGT complexes formed on lesion-free DNAs that model the unmodified parts of the genome. We used a new approach to resolve nearest neighbor (nn) and long-range (lr) components from the ensemble-average cooperativity, ωave. We found that ...


A Comparison Of Nucleosome Organization In Drosophila Cell Lines, Rebecca L. Martin, John Maiorano, Greg J. Beitel, John F. Marko, Graham Mcvicker, Yvonne N. Fondufe-Mittendorf Jun 2017

A Comparison Of Nucleosome Organization In Drosophila Cell Lines, Rebecca L. Martin, John Maiorano, Greg J. Beitel, John F. Marko, Graham Mcvicker, Yvonne N. Fondufe-Mittendorf

Molecular and Cellular Biochemistry Faculty Publications

Changes in the distribution of nucleosomes along the genome influence chromatin structure and impact gene expression by modulating the accessibility of DNA to transcriptional machinery. However, the role of genome-wide nucleosome positioning in gene expression and in maintaining differentiated cell states remains poorly understood. Drosophila melanogastercell lines represent distinct tissue types and exhibit cell-type specific gene expression profiles. They thus could provide a useful tool for investigating cell-type specific nucleosome organization of an organism’s genome. To evaluate this possibility, we compared genome-wide nucleosome positioning and occupancy in five different Drosophila tissue-specific cell lines, and in reconstituted chromatin, and ...


Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver Apr 2017

Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination ...


Liquid Crystal Phase Behavior Of A Dna Dodecamer And Sunset Yellow, Joseph Theis Jan 2017

Liquid Crystal Phase Behavior Of A Dna Dodecamer And Sunset Yellow, Joseph Theis

Undergraduate Honors Theses

The organic molecule Sunset Yellow, a chromonic dye, and reverse Dickerson dodecamer DNA, a self-complementary, 12 base pair strand of nucleic acids, both self-assemble into rod shaped aggregates that exhibit liquid crystal phases in solution. The sunset yellow molecules and the nano-DNA duplexes have similar structure with hydrophobic cores and peripheral hydrophilic ions. The focus of this research is on mixtures of these two aggregates in miscible liquid crystal states and the phase separation that occurs at higher concentrations in the columnar phase. The structure and phase space of this mixture was determined using polarized optical microscopy and x-ray diffraction ...


Silica Nanoparticles For The Delivery Of Dna And Rnai In Cancer Treatment, Michael Aaron Vrolijk Jan 2017

Silica Nanoparticles For The Delivery Of Dna And Rnai In Cancer Treatment, Michael Aaron Vrolijk

Graduate College Dissertations and Theses

DNA and interfering RNA (RNAi) – short interfering RNA (siRNA) and micro RNA (miRNA) – are promising new cancer therapies, especially for drug resistant lines. However, they require a delivery system in vivo to prevent degradation and off target effects. Silica based nanoparticles, both solid and mesoporous, are a promising option due to their biocompatibility, ease of preparation and morphology control, reproducibility, and facile addition of functional groups including targeting ligands.

After a brief introduction to cancer treatment and review of the current nanoparticle treatments undergoing clinical trials, this thesis details the many methods explored over the past ten years to fine-tune ...


The Functions Of The Cid And Lrg Operons In S. Aureus Programmed Cell Death, Xinyan Zhang Dec 2016

The Functions Of The Cid And Lrg Operons In S. Aureus Programmed Cell Death, Xinyan Zhang

Theses & Dissertations

Staphylococcus aureus cid/lrg operons regulate the formation of S.aureus biofilm formation and programmed cell death based on previous in vivo work done in Dr. Bayles's lab. cid operon, which encodes CidA/CidB/CidC proteins, has been shown to be an effector in leading to the lysis and death of the S.aureus; While lrg operon, encoding LrgA and LrgB proteins, is an inhibitor of the lysis and death. Recent studies suggest that CidA behaves like holin proteins from bacterial phage, by increasing the murein hydrolysis activity under aerobic culturing conditions. LrgA, together with LrgB, appears ...


Coarse-Grained Simulations Of The Self-Assembly Of Dna-Linked Gold Nanoparticle Building Blocks, Charles Wrightsman Armistead Dec 2016

Coarse-Grained Simulations Of The Self-Assembly Of Dna-Linked Gold Nanoparticle Building Blocks, Charles Wrightsman Armistead

Theses and Dissertations

The self-assembly of nanoparticles (NPs) of varying shape, size, and composition for the purpose of constructing useful nanoassemblies with tailored properties remains challenging. Although progress has been made to design anisotropic building blocks that exhibit the required control for the precise placement of various NPs within a defined arrangement, there still exists obstacles in the technology to maximize the programmability in the self-assembly of NP building blocks. Currently, the self-assembly of nanostructures involves much experimental trial and error. Computational modeling is a possible approach that could be utilized to facilitate the purposeful design of the self-assembly of NP building blocks ...


The Large Terminase Dna Packaging Motor Grips Dna With Its Atpase Domain For Cleavage By The Flexible Nuclease Domain, Brendan J. Hilbert, Janelle A. Hayes, Nicholas P. Stone, Rui-Gang Xu, Brian A. Kelch Oct 2016

The Large Terminase Dna Packaging Motor Grips Dna With Its Atpase Domain For Cleavage By The Flexible Nuclease Domain, Brendan J. Hilbert, Janelle A. Hayes, Nicholas P. Stone, Rui-Gang Xu, Brian A. Kelch

University of Massachusetts Medical School Faculty Publications

Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the ATPase that powers DNA translocation and an endonuclease that cleaves the concatemeric genome both at initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage is still mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in ...


Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed Sep 2016

Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed

All Dissertations, Theses, and Capstone Projects

Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important ...


Hemi-Methylated Dna Regulates Dna Methylation Inheritance Through Allosteric Activation Of H3 Ubiquitylation By Uhrf1, Joseph S. Harrison, Evan M. Cornett, Dennis Goldfarb, Paul A. Darosa, Zimeng M. Li, Feng Yan, Bradley M. Dickson, Angela H. Guo, Daniel V. Cantu, Lilia Kaustov, Peter J. Brown, Cheryl H. Arrowsmith, Dorothy A. Erie, Michael B. Major, Rachel E. Klevit, Krzysztof Krajewski, Brian Kuhlman, Brian D. Strahl, Scott B. Rothbart Sep 2016

Hemi-Methylated Dna Regulates Dna Methylation Inheritance Through Allosteric Activation Of H3 Ubiquitylation By Uhrf1, Joseph S. Harrison, Evan M. Cornett, Dennis Goldfarb, Paul A. Darosa, Zimeng M. Li, Feng Yan, Bradley M. Dickson, Angela H. Guo, Daniel V. Cantu, Lilia Kaustov, Peter J. Brown, Cheryl H. Arrowsmith, Dorothy A. Erie, Michael B. Major, Rachel E. Klevit, Krzysztof Krajewski, Brian Kuhlman, Brian D. Strahl, Scott B. Rothbart

College of the Pacific Faculty Articles

The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the ...


Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li Aug 2016

Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li

CSE Journal Articles

We introduce the idea of constructing hypothetical evolutionary trees using an incremental algorithm that inserts species one-by-one into the current evolutionary tree. The method of incremental phylogenetics by repeated insertions lead to an algorithm that can be used on DNA, RNA and amino acid sequences. According to experimental results on both synthetic and biological data, the new algorithm generates more accurate evolutionary trees than the UPGMA and the Neighbor Joining algorithms.


Epigenetic Regulation Of Gene Expression During Spermatogenesis, Karishma Nayak May 2016

Epigenetic Regulation Of Gene Expression During Spermatogenesis, Karishma Nayak

Senior Honors Projects

In the US livestock production industry, improving reproductive efficiency will improve animal welfare and maintain reasonable costs of meat and milk for consumers. In recent research, abnormalities in epigenetic markers in sperm during spermatogenesis, has been linked to male subfertility in many species. Epigenetics is the study of changes in organisms caused by modifications of gene expression, including DNA methylation, rather than alteration of the genetic code itself. When this process is disturbed, it can negatively impact semen therefore decreasing its fertility. Through further research on how DNA methylation influences gene expression during spermatogenesis and its impact on sperm quality ...


The Pcna-Associated Protein Pari Negatively Regulates Homologous Recombination Via The Inhibition Of Dna Repair Synthesis, Peter Burkovics, Lili Dome, Szilvia Juhasz, Veronika Altmannova, Marek Sebesta, Martin Pacesa, Kasper Fugger, Claus Storgaard Sorensen, Marietta Y W T Lee, Lajos Haracska, Lumir Krejci Apr 2016

The Pcna-Associated Protein Pari Negatively Regulates Homologous Recombination Via The Inhibition Of Dna Repair Synthesis, Peter Burkovics, Lili Dome, Szilvia Juhasz, Veronika Altmannova, Marek Sebesta, Martin Pacesa, Kasper Fugger, Claus Storgaard Sorensen, Marietta Y W T Lee, Lajos Haracska, Lumir Krejci

NYMC Faculty Publications

Successful and accurate completion of the replication of damage-containing DNA requires mainly recombination and RAD18-dependent DNA damage tolerance pathways. RAD18 governs at least two distinct mechanisms: translesion synthesis (TLS) and template switching (TS)-dependent pathways. Whereas TS is mainly error-free, TLS can work in an error-prone manner and, as such, the regulation of these pathways requires tight control to prevent DNA errors and potentially oncogenic transformation and tumorigenesis. In humans, the PCNA-associated recombination inhibitor (PARI) protein has recently been shown to inhibit homologous recombination (HR) events. Here, we describe a biochemical mechanism in which PARI functions as an HR regulator ...


Dna Sequencing Activity, Sarah O'Leary-Driscoll Feb 2016

Dna Sequencing Activity, Sarah O'Leary-Driscoll

Sequencing & Genome Mining

This activity is meant to introduce students to basic DNA sequencing techniques. Using a hands-on approach helps them understand the fundamentals of what is happening in the lab, and the questions that accompany the activity can lead to more in depth discussions about sequencing, and the development of the next generation sequencing techniques.


A Novel Forensic Dna Profiling Method Based On Molecular Beacons Without Dna Purification, Benjamin C. Shaw Jan 2016

A Novel Forensic Dna Profiling Method Based On Molecular Beacons Without Dna Purification, Benjamin C. Shaw

Online Theses and Dissertations

Analysis of polymorphisms in nucleic acid sequences provides the basis for identification of individuals and their genetic deficiencies. Currently, the accepted method of analysis for profiling is Short Tandem Repeat (STR) profiling. This is a lengthy process, typically taking up to 3 days. The time necessary to generate an STR profile, along with the ever-increasing reliance on DNA to solve crimes, has led to a large DNA sample backlog, with violent crime turnaround taking an average of 103 days. The time and resource investment required for STR analysis is significant, and not all samples generate useful profiles.

The current methods ...


Aptameric Sensors: In Vitro Selection Of Dna That Binds Bromocresol Purple, Derek B. Miller Jan 2016

Aptameric Sensors: In Vitro Selection Of Dna That Binds Bromocresol Purple, Derek B. Miller

Honors Undergraduate Theses

Aptamers being used as sensors is an emerging field that has capabilities of being tomorrow’s diagnostic tools. As aptameric sensors have become more popular, their visualization systems have been limited. The majority of today’s aptameric sensors require expensive machinery such as a fluorometer in order to visualize results. We propose a system that will cut the need for instrumentation and be detected via the naked eye. With the selection of an aptamer to bind the pH indicating dye bromocresol purple (BCP) this may be achieved. When rendered active, the binding towards BCP will facilitate a color change from ...


Instability At Trinucleotide Repeat Dnas, Rujuta Yashodhan Gadgil Jan 2016

Instability At Trinucleotide Repeat Dnas, Rujuta Yashodhan Gadgil

Browse all Theses and Dissertations

Trinucleotide repeats (TNRs) are sequences prone to formation of non-B DNA structures and mutations; undergo expansions in vivo to cause various inherited neurodegenerative diseases. Hairpin structures formed during DNA replication or repair can cause replication fork stalling and if left unrepaired could cause single or double strand DNA breaks. To test and study this hypothesis we have devised a novel two color marker gene assay to detect DNA breaks at TNRs. By inducing replication stress our results show that TNRs are prone to DNA strand breaks and it is dependent on the repeat tract length. Double strand breaks at structured ...


Modeling Technologies And Methods For Dna Origami, Brian Thomas Nakayama Jan 2016

Modeling Technologies And Methods For Dna Origami, Brian Thomas Nakayama

Graduate Theses and Dissertations

The creation of correctly assembling DNA origami often requires several iterations wherein a researcher tries and troubleshoots an incremental design. In each iteration there exists one or more costly failures that often take immense time or materials to find. These failures occur in part due to a lack of in-depth understanding of how DNA origami self-assembles and functions. To aid researchers in developing correct DNA origami designs, this thesis describes the creation of a DNA origami failure catalog as well as models for elucidating as-of-yet only partially understood properties of DNA origami. The failure catalog helps laboratory scientists gather requirements ...


X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar Jan 2016

X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar

Doctoral Dissertations

We think of DNA as double-stranded helices (duplex), but the polymer exists in many conformations. Several triplex and quadruplex DNA structures can be formed in laboratory settings and exist in nature. This thesis first provides a brief description of the nature of the order in arrays of duplex DNA under biologically relevant molecular crowding conditions. Then we compare the duplex DNA mesophases with the corresponding liquid crystalline phase behavior of the triplex and quadruplex DNA analogues. In particular, we focus on G-quadruplexes.

Observed in the folds of guanine-rich oligonucleotides, G-quadruplex structures are based on G-quartets formed by hydrogen bonding and ...