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All Subjects: Chemistry

Syntheses of Non-Canonical Amino Acids Containing Stilbene

Description

Non-canonical amino acids (NCAAs) can be used in protein chemistry to determine their structures. A common method for imaging proteins is cryo-electron microscopy (cryo-EM) which is ideal for imaging proteins that cannot be obtained in large quantities. Proteins with indistinguishable features are difficult to image using this method due to the large size requirements, therefore antibodies designed specifically for binding these proteins have been utilized to better identify the proteins. By using an existing antibody that binds to stilbene, NCAAs containing this molecule can be used as a linker between proteins and an antibody. Stilbene containing amino acids can be integrated into proteins to make this process more access able. In this paper, synthesis methods for various NCAAs containing stilbene were proposed. The resulting successfully synthesized NCAAs were E)-N6-(5-oxo-5-((4-styrylphenyl) amino) pentanoyl) lysine, (R,E)-2-amino-3-(5-oxo-5-((4-styrylphenyl)amino)pentanamido)propanoic acid, (E)-2-amino-5-(5-oxo-5-((4-styrylphenyl) amino) pentanamido) pentanoic acid. A synthesis for three more shorter amino acids, (R,E)-2-amino-3-(3-oxo-3-((4-styrylphenyl) amino) propanamido) propanoic acid, (E)-2-amino-5-(3-oxo-3-((4-styrylphenyl) amino) propanamido) pentanoic acid, and (E)-N6-(3-oxo-3-((4-styrylphenyl) amino) propanoyl) lysine, is also proposed.

ContributorsJenkins, Bryll (Author) / Mills, Jeremy (Thesis director) / Ghirlanda, Giovanna (Committee member) / Nannenga, Brent (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)

Created2022-05

High-Resolution 3D Printed Microfluidic Devices for Dielectrophoretic Manipulation of Proteins

Description

Insulator-based dielectrophoresis (iDEP) has attracted considerable attention due to its ability to precisely capture and manipulate nanoparticles and biomolecules. A distinctive approach for effective manipulation of nanometer-sized proteins employing iDEP technique by generating higher electric field (E) and gradient (??2) in the iDEP microfluidic devices is delineated. Strategies to generate higher ??2 in the iDEP devices were outlined using numerical simulations. Intriguingly, the numerical simulation results demonstrated that by decreasing the post-to-post gap in the iDEP microfluidic devices, the ??2 was increased by ⁓12 fold. Furthermore, the inclusion of channel constrictions, such as rectangular constriction or curved constriction into the straight channel iDEP microfluidic device led to a significant increase in ??2. In addition, the inclusion of rectangular constrictions in the straight channel iDEP microfluidic device resulted in a greater increase in ??2 compared to the incorporation of curved constrictions in the same device. Moreover, the straight channel device with horizontal post-to-post gap of 20 μm and vertical post-to-post gap of 10 μm generated the lowest ??2 and the ??2 was uniform across the device. The rectangular constriction device with horizontal and vertical post-to-post gap of 5 μm generated the highest ??2 and the ??2 was non-uniform across the device. Subsequently, suitable candidate devices were fabricated using soft lithography as well as high resolution 3D printing and the DEP behavior of ferritin examined under various experimental conditions. Positive streaming DEP could be observed for ferritin at low frequency in the device generating the lowest ??2, whereas at higher frequency of 10 kHz no DEP trapping characteristics were apparent in the same device. Importantly, in the device geometry resulting in the highest ??2 at 10 kHz, labeled ferritin exhibited pDEPtrapping characteristics. This is an indication that the DEP force superseded diffusion and became the dominant force.

ContributorsMAHMUD, SAMIRA (Author) / Ros, Alexandra (Thesis advisor) / Borges, Chad (Committee member) / Mills, Jeremy (Committee member) / Arizona State University (Publisher)

Created2024

Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures

Description

Since the inception of DNA nanotechnology, DNA has found itself poised as one of the most robust self-assembling building blocks due to its well understood double helix structure formed by two anti-parallel strands of DNA held together by hydrogen bond from nucleobases which also provides the material programmability due to the well-understood Watson Crick base pairing rules. These capabilities have led to the exponential increase in publications showing off intricate and remarkable designs alongside ever-expanding applications. However, as the field expands there is an apparent lack of chemical diversity and functionality. To combat this my research focused on creating hybrid peptide oligonucleotide conjugates (POC) where the conjugated peptide could add chemical and structural diversity using the 20 canonical amino acids and various peptide secondary structures. In this work, I conjugate DNA to the self-assembling peptide building block the coiled coil. The coiled coil motif is formed from the self-assembly of two or more α-helical peptides and, like DNA, the coiled coil has well understood programmability. Together as a conjugate, the DNA and coiled coil, create a new self-assembling building block capable of two orthogonal self-assembling modes that can work in tandem. In this work, I used DNA coiled coil conjugates to show the capability to create first of their kind hybrid DNA/coiled coil one-dimensional fibers (chapter 2), integrate proteins (chapter 3), and to create hybrid cage structures (chapter 4). Finally, a POC hydrogel is created using the polypeptide gelatin with DNA crosslinks to create a reversible stiffening gel using toe-hold mediated strand displacement (chapter 5).

ContributorsBuchberger, Alex Richard (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Mills, Jeremy (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)

Created2021