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Published August 2005 | public
Journal Article

Parallel Selections In Vitro Reveal a Preference for 2′–5′ RNA Ligation upon Deoxyribozyme-Mediated Opening of a 2′,3′-Cyclic Phosphate


We previously used in vitro selection to identify Mg²⁺-dependent deoxyribozymes that mediate the ligation reaction of an RNA 5′-hydroxyl group with a 2′,3′-cyclic phosphate. In these efforts, all of the deoxyribozymes were identified via a common in vitro selection strategy, and all of the newly formed RNA linkages were non-native 2′–5′ phosphodiester bonds rather than native 3′–5′ linkages. Here we performed several new selections in which the relative arrangements of RNA and DNA were different as compared with the earlier studies. In all cases, we again find deoxyribozymes that create only 2′–5′ linkages. This includes deoxyribozymes with an arrangement that favors 3′–5′ linkages for a different chemical reaction, that of a 2′,3′-diol plus 5′-triphosphate. These data indicate a strong and context-independent chemical preference for creating 2′–5′ RNA linkages upon opening of a 2′,3′-cyclic phosphate with a 5′-hydroxyl group. Preliminary assays show that some of the newly identified deoxyribozymes have promise for ligating RNA in a sequence-general fashion. Because 2′,3′-cyclic phosphates are the products of uncatalyzed RNA backbone cleavage, their ligation reactions may be of direct relevance to the RNA World hypothesis.

Additional Information

© 2005 Springer. Received: 15 November 2004 / Accepted: 2 February 2005. This research was supported by the Burroughs Wellcome Fund (New Investigator Award in the Basic Pharmacological Sciences), the March of Dimes Birth Defects Foundation (Research Grant 5-FY02-271), the National Institutes of Health (GM-65966), the American Chemical Society Petroleum Research Fund (38803-G4), and the UIUC Department of Chemistry (all to S.K.S.). S.K.S. is the recipient of a fellowship from The David and Lucile Packard Foundation. We thank Yangming Wang and other members of the Silverman lab for helpful discussions.

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