Development and execution of selection methods for lysine-acylating deoxyribozymes

Przybyla, John J (Jack)

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https://hdl.handle.net/2142/115829 Copy

Description

Title

Development and execution of selection methods for lysine-acylating deoxyribozymes

Author(s)

Przybyla, John J (Jack)

Issue Date

2022-04-29

Director of Research (if dissertation) or Advisor (if thesis)

Silverman, Scott K

Department of Study

Biochemistry

Discipline

Biochemistry

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• DNAzyme
• Novel Catalyst
• In Vitro selection
• Lysine acylation
• DNA catalysis

Abstract

DNA catalysts (deoxyribozymes, or DNAzymes) represent an exciting possibility in the world of novel catalysis. Their ability to be amplified via polymerase chain reaction (PCR) allows for in vitro selection of DNAzymes that catalyze specific reactions. Through the use of in vitro selection, DNAzymes have been identified for a growing number of reactions, including lysine side chain acylation. However, these acylating DNAzymes make use of model substrates that are attached to a complementary DNA anchor that allows for recruitment to a DNAzyme active site. These highly specific substrates do not resemble the large protein or small-molecule substrates that act as valuable targets for novel catalysts. As a result, these DNAzymes do not yet possess the level of utility that makes novel catalysts exciting. This body of work, conducted in the Silverman lab at UIUC, looks to build upon previous discoveries by establishing a selection scheme for lysine acylation in a non-anchored peptide. This includes the development of more diverse and complex substrates, the development and testing of selection conditions, and the development of a necessary “capture” step to enable the selection process. As a precursor to my ultimate project, my contributions towards the identification of amine acylating, and later lysine side chain acylating DNAzymes, will also be included. At time of writing, the selection methods discussed here are being employed in the Silverman lab to identify DNAzymes that catalyze the acylation of lysine on a non-anchored peptide. If these DNAzymes are successfully identified, they would act as another crucial step towards the identification of “useful” novel DNA catalysts.

Graduation Semester

2022-05

Type of Resource

Thesis

Copyright and License Information

Copyright 2022 John Przybyla

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