Crystal structure of a DNA catalyst

• Published in: Nature (London) Vol. 529; no. 7585; pp. 231 - 234
• Main Authors: Ponce-Salvatierra, Almudena, Wawrzyniak-Turek, Katarzyna, Steuerwald, Ulrich, Höbartner, Claudia, Pena, Vladimir
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.01.2016; Nature Publishing Group
• Subjects: 631/45/535/1266; 631/92/610; Base Sequence; Biocatalysis; Catalysis; Catalysts; Catalytic Domain; Catalytic RNA; Chemical reactions; Crystal structure; Crystallography, X-Ray; Crystals; Deoxyribonucleic acid; Deoxyribose - chemistry; Deoxyribose - metabolism; DNA; DNA, Catalytic - chemical synthesis; DNA, Catalytic - chemistry; DNA, Catalytic - metabolism; Enzymes; Genetic research; Humanities and Social Sciences; Influence; Kinetics; letter; Models, Molecular; Molecular Sequence Data; Monosaccharides; multidisciplinary; Mutagenesis; Nucleic Acid Conformation; Nucleic acids; Nucleotides - chemistry; Nucleotides - metabolism; Polynucleotide Ligases - chemistry; Polynucleotide Ligases - metabolism; RNA - chemistry; RNA - metabolism; RNA Folding; Science; Structure; Substrate Specificity; Sugars; Germany
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature16471

Both DNA and RNA molecules have been shown to exhibit catalytic activity, but only the structure of catalytic RNAs has previously been determined; here the structure of an RNA-ligating DNA in the post-catalytic state is solved. Structure of a deoxyribozyme Both DNA and RNA molecules are foldable and can adopt conformations that exhibit catalytic activity. While the structures of various catalytic RNAs — or ribozymes — have been determined, DNA enzymes have proved more difficult. Claudia Höbartner and colleagues have now solved the crystal structure of the synthetic single-stranded DNA deoxyribozyme 9DB1 at 2.8 Å resolution. 9DB1 is an RNA ligase catalysing phosphodiester bond formation between 3′-hydroxyl and the 5′-triphosphate termini of two RNA strands. The structure reveals three-dimensional complexity comparable to that adopted by RNA, but with differences reflecting the specific properties of deoxyribose. Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) 1 or synthetic genetic polymers 2 . In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage 3 . DNA-catalysed reactions include RNA and DNA ligation in various topologies 4 , 5 , hydrolytic cleavage 6 , 7 and photorepair of DNA 8 , as well as reactions of peptides 9 , 10 and small molecules 11 , 12 . In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold 13 . Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14 ) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms.