Biomedical Engineering ETDs

Publication Date

Summer 8-1-2024

Abstract

This dissertation explores the use of intrinsically disorder proteins (IDPs) in biomedical applications related to the detection and biosensing of nucleic-acid species. We engineer several low critical solution temperature (LCST) nucleic-acid binding elastin-like polypeptides (ELPs) as model IDPs and study their potential in biomedical application via interactions with short single-stranded (ss) DNA, tRNA and viral RNAs. First, we engineer a simple polycationic ELP capable of recruiting DNA on demand in a DNA-protein-rich condensate via LLPS. Moreover, we develop a modified Flory-Huggins theory to quantify the partitioning of DNA and protein upon coacervate formation with and without salts. We then design more robust NA-binding ELPs for use in the detection of NA pathogens such as NA extraction (NAE) or isolation to investigate the potential use of NA-binding ELPs as molecular chaperones of relevant DNA reactions. Our findings suggest that the genetically engineered IDPs we designed can concentrate complementary and structurally complex DNA strands in a biomolecular condensate to accelerate the kinetics of the reaction. Altogether, we show that IDPs can have a major impact on downstream processes involved in the process of NA testing.

Language

English

Keywords

Intrinsically disordered proteins, elastin-like polypeptides, membraneless organelles, nucleic acid extraction, nucleic acid binding, nucleic acid chaperones, strand annealing

Document Type

Dissertation

Degree Name

Biomedical Engineering

Level of Degree

Doctoral

Department Name

Biomedical Engineering

First Committee Member (Chair)

Dr. Nichlaus J. Carroll

Second Committee Member

Dr. Gabriel P. López

Third Committee Member

Dr. David S. Peabody

Fourth Committee Member

Dr. Andrew P. Shreve

Comments

This dissertation was submitted for an embargo.

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Available for download on Thursday, August 01, 2024

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