title: Functional Hallmarks of a Catalytic DNA that Makes Lariat RNA.
abstract: Catalytic DNAs, also known as deoxyribozymes, are of practical value for the synthesis of structurally or topologically complex RNAs, but little is known about the molecular details of DNA catalysis. We have investigated a deoxyribozyme that catalyzes the formation of a specific intramolecular 2',5'-phosphodiester bond to produce lariat RNA, which is an important biological intermediate in eukaryotic mRNA splicing. The results of combinatorial mutation interference analysis (CoMA) allowed us to shrink the catalytic core to 70 % of its original length and revealed that the essential part of the deoxyribozyme sequence contained more than 50 % guanosines. Nucleotide analogue interference mapping (dNAIM) and dimethyl sulfate interference (DMSi) experiments provided atomic details of individual guanosine functional groups. Additional spectroscopic experiments and structural probing data identified conformational changes upon metal-ion binding and catalysis. Overall, this comprehensive analysis of the DNA-catalyzed reaction has provided specific insights into the synthesis of 2',5'-branched RNA, and suggested the general features of deoxyribozymes that catalyze nucleic acid ligation reactions.
authors.affiliation: Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.|Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Javadi-Zarnaghi
authors.affiliation: Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany. Claudia.hoebartner@chemie.uni-goettingen.de.|Institute for Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany. Claudia.hoebartner@chemie.uni-goettingen.de.
authors.forename: Claudia
authors.initials: C
authors.lastname: Höbartner
mesh_terms: D021881:DNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D006151:Guanosine / Q000031:analogs & derivatives* / Q000737:chemistry*; D008026:Ligation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012326:RNA Splicing
chemical_list: D021881:DNA, Catalytic; D006151:Guanosine; D012313:RNA
keywords: DNA catalysis; DNA structures; RNA; deoxyribozymes; nucleic acids