Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2′,3′-cyclic phosphate RNA substrates

Diana M. Kost, Joseph P. Gerdt, P. I. Pradeepkumar, Scott K. Silverman

Research output: Contribution to journalArticle

Abstract

Our previous efforts have used in vitro selection to identify numerous Zn2+-dependent deoxyribozymes that ligate two RNA substrates with reaction at a 2′,3′-cyclic phosphate. Each deoxyribozyme creates one of several different RNA linkages, including native 3′-5′ and non-native 2′-5′ phosphodiester bonds as well as many unnatural linkages. In this report, we describe experiments to reveal design aspects of the selection strategy that favor site-selective and regioselective synthesis of native 3′-5′ RNA linkages. The results also reveal that an explicit selection pressure for RNA substrate sequence generality must be developed if the deoxyribozymes are to have practical generality.

Original languageEnglish (US)
Pages (from-to)4391-4398
Number of pages8
JournalOrganic and Biomolecular Chemistry
Volume6
Issue number23
DOIs
StatePublished - Nov 24 2008

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Catalytic DNA
Regioselectivity
linkages
Ligation
phosphates
selectivity
Phosphates
RNA
Substrates
Pressure
synthesis
Direction compound
Experiments

ASJC Scopus subject areas

  • Biochemistry
  • Physical and Theoretical Chemistry
  • Organic Chemistry

Cite this

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2′,3′-cyclic phosphate RNA substrates. / Kost, Diana M.; Gerdt, Joseph P.; Pradeepkumar, P. I.; Silverman, Scott K.

In: Organic and Biomolecular Chemistry, Vol. 6, No. 23, 24.11.2008, p. 4391-4398.

Research output: Contribution to journalArticle

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