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Deoxyribozymes with coenzyme‐dependent RNA‐phosphoesterase activity
Author(s) -
Carranza Dorn L,
Kane Robert R
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.5.a904
Subject(s) - deoxyribozyme , cofactor , chemistry , combinatorial chemistry , rna , nucleic acid , stereochemistry , linker , small molecule , coenzyme a , biochemistry , catalysis , dna , rational design , enzyme , biology , gene , reductase , genetics , computer science , operating system
In the present research, we have designed and synthesized small‐molecule cofactors (coenzymes) that could be used by catalytic DNA molecules (deoxyribozymes) in the hydrolysis of an RNA substrate. Each of the putative coenzymes is a small synthetic compound containing two imidazole moieties attached through amide bonds to a diacid linker. Parallel combinatorial in vitro selection and evolution of small randomized DNAs was performed in the presence of the coenzymes in order to isolate novel deoxyribozyme/coenzyme couples. Catalytic reactions with the deoxyribozymes showed enhanced catalytic activity that was selectively dependent on the coenzyme used in the selection. Catalytic rates obtained for the deoxyribozyme/coenzyme systems were found to be dependent on pH, with calculated pKa values that suggest the participation of the coenzyme imidazoles. In conclusion, we have demonstrated that combinatorial selection techniques can be used to select for coenzyme‐dependent deoxyribozymes. This rapid and efficient methodology complements rational design approaches, and provides a unique opportunity for the study of various aspects of deoxyribozyme/coenzyme design and for the pursuit of fundamental investigations into nucleic acid/small‐molecule interactions. Research supported by Robert A. Welch Foundation (Grant #1355)