Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.
Our previous efforts have used in vitro selection to identify numerous Zn(2+)-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.
Kost
Diana M
DM
Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Gerdt
Joseph P
JP
Pradeepkumar
P I
PI
Silverman
Scott K
SK
D001665:Binding Sites; D021881:DNA, Catalytic / Q000378:metabolism*; D010710:Phosphates / Q000737:chemistry* / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D013237:Stereoisomerism; D013379:Substrate Specificity; D015032:Zinc / Q000378:metabolism*
D021881:DNA, Catalytic; D010710:Phosphates; D012313:RNA; D015032:Zinc