DNA as a Catalyst and as a Sensor: Investigating the Structure of the Ty1 Retrotransposition Intermediate and the Utility of Dna-Based Biosensors

The catalytic and binding properties of functional nucleic acids have been exploited to investigate key biochemical questions and to detect small molecules for diagnostic applications. Catalytic DNA (deoxyribozymes) can catalyze many different chemical reactions such as RNA ligation, RNA cleavage, DNA phosphorylation, DNA ligation, DNA adenylation, nucleopeptide formation, Diels-Alder reaction, and porphyrin metalation. RNA ligation is catalyzed by using either an internal 2'-hydroxyl, a terminal 3'-hydroxyl or a terminal 2'-hydroxyl to attack a 5'-triphosphate, synthesizing a variety of RNA linkages: 2',5'-branch, 3'-5'-linear, or 2'-5'-linear. RNA-branching deoxyribozymes can be used to study the role of specific biochemical intermediates, such as the putative 2',5'-branched RNA intermediate in Ty1 retrotransposition. Aptamers are three-dimensional structures of single-stranded DNA that can bind small molecules with both high affinity and selectivity. Aptamers are isolated by in vitro selection from random libraries of single-stranded sequences by their ability to recognize a particular target. The aptamer can then be developed into a sensor, which can be used as a diagnostic tool for the detection of a specific target.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biochemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2014

Author dc:creator

• Pratico, Elizabeth D.

Contributors dc:contributor

• Silverman, Scott K.

• Chemistry, Biochemistry

Identifier

(UMI)AAI3337891

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/72336