Deoxyribozymes That Prepare Branched and Linear RNA by Ligation

An ongoing challenge for deoxyribozyme-mediated RNA ligations has been synthesis of native 3'-5' phosphodiester linkages. Previously, reactions of 5'-triphosphate RNA have provided mostly 2',5'-branched RNA. Here we report two new in vitro selection strategies designed to favor formation of the native linkage. The first strategy controls the regioselectivity by placing the incipient linkage within a DNA:RNA duplex region, such that 3'-5' is favored over 2'-5' both thermodynamically and kinetically. The second strategy makes use of a known deoxyribozyme that reacts only with 3'-5' RNA linkages. Both strategies were successful in making the native 3'-5' RNA linkage. Two deoxyribozymes, 9DB1 and 7DE5, from the second strategy have very few sequence requirements at the ligation junction. These deoxyribozymes will be useful as biochemical tools to study catalytic nucleic acids.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2015

Author dc:creator

• Coppins, Rebecca Lyn

Contributors dc:contributor

• Scott Silverman

• Chemistry, Biochemistry

Language dc:language

eng

Identifier

(MiAaPQ)AAI3198957

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/84183