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Full-Text Articles in Molecular Biology

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 ...


Using Intrinsic Properties Of Polyaniline To Sense Expression Of The Microrna Let-7, Jared N. Gloria May 2016

Using Intrinsic Properties Of Polyaniline To Sense Expression Of The Microrna Let-7, Jared N. Gloria

Honors Theses

MicroRNAs are approximately 22-nucleotide long RNA molecules that function through decay and translational repression of messenger RNA. The microRNA let-7 is found to play a role in maintaining the fate of differentiated cells in humans. Thus, expression level of this microRNA is a reliable biomarker of tumor cell phenotype. However, there are significant limitations in the current profiling techniques of microRNA. The current methods like northern blotting, microarrays, RT-PCR, or using locked nucleic acid (LNA) for in-situ hybridization are either laborious, semi-quantitative, or expensive. In this research we try to address this issue by developing a fast, specific, and inexpensive ...


Utilizing Synthetic Tools To Address Biological Issues, Marshall Scott Padilla May 2016

Utilizing Synthetic Tools To Address Biological Issues, Marshall Scott Padilla

Undergraduate Honors Theses

With the advent of chemoselective reactions and unnatural amino acids (UAAs), the fields of molecular biology and organic synthesis are merging. Researchers are developing synthetic tools and producing small molecules that are able to affect and investigate large biomolecules and complex living systems. This thesis undertakes a survey of synthetic techniques to develop novel tools that can be employed to address a variety of relevant biological questions. Specifically, we are investigating alternatives and improvements to caging groups, including photoreversible azobenzene UAAs and an UAA caging group possessing a bioorthogonal handle. Also, we are developing a novel system to undergo copper-free ...


Investigation Of Unnatural Amino Acids As A Means To Modulate Protein Function, Taylor Harrison Jacobs May 2016

Investigation Of Unnatural Amino Acids As A Means To Modulate Protein Function, Taylor Harrison Jacobs

Undergraduate Honors Theses

In order to elucidate the biological processes that occur in everyday life, chemical biologists have developed technologies that allow the study of a various biological systems. Bioorthogonal chemistry is an ever-growing technology that involves performing chemical reactions with biological systems that do not rely on existing biological chemistries. In this work we attempt to develop and characterize novel bioorthognal chemistries that further expand the utility of this field. Additionally, we explore the utility of fluorescent probes in labeling applications. Finally, we attempt to create novel methods of control for a gene-editing protein using light as a mechanism of regulation.


Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens Apr 2016

Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens

Undergraduate Honors Theses

One way to study disease is to model specific biological reactions or processes involved in the generation of the disease in terms of a system of differential equations. The equations, called kinetic rate laws, are often non-linear and high order, making them difficult to solve. By approximating equations in complex biological networks as linear first order reactions, we can solve large sets of equations using computational software, such as MATLAB, to determine general trends in the change of molecular concentrations over time. These trends can tell us details about the disease and direct us toward areas worthy of further investigation ...


Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann Jan 2016

Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann

Doctoral Dissertations

Copper catalyzed cycloaddition of terminal alkynes and azides has revolutionized the field of bioconjugate chemistry. Unfortunately, typical copper catalysts are known to disrupt relevant biological systems, so it has become necessary to develop new, copper-free methods that are less cytotoxic. particular interest are "click" probes which can be activated with an outside light source, giving the user spatial and temporal control over the system being investigated. We have developed a method in which an aryl diazonium salt is rapidly generated using photolysis of the triazene functional group, and subsequently coupled with an electron rich aromatic nucleophile to yield an azobenzene ...


A Computationally Designed Protein-Ligand Interaction Is Mechanically Robust, William John Van Patten Jan 2016

A Computationally Designed Protein-Ligand Interaction Is Mechanically Robust, William John Van Patten

Undergraduate Honors Theses

Protein-ligand interactions govern essential and ubiquitous biological processes such as immune response and gene regulation. Recently, the first computationally designed ligand-binding protein named DIG10.3 was developed by the Baker lab at the University of Washington. This artificially designed (rather than naturally evolved) ligand binding protein exhibited high affinity and selectivity to its target ligand, Digoxigenin (Dig). Such computationally designed ligand-binders offer promising capabilities in diagnostics and therapeutics for a wide range of diseases. By applying a mechanical force to a single DIG10.3::Digoxigenin interaction through atomic force microscope (AFM)-based single-molecule force spectroscopy (SMFS) we can extract unique ...