DNAmoreDB, a database of DNAzymes

Abstract

Deoxyribozymes, DNA enzymes or simply DNAzymes are single-stranded oligo-deoxyribonucleotide molecules that, like proteins and ribozymes, possess the ability to perform catalysis. Although DNAzymes have not yet been found in living organisms, they have been isolated in the laboratory through in vitro selection. The selected DNAzyme sequences have the ability to catalyze a broad range of chemical reactions, utilizing DNA, RNA, peptides or small organic compounds as substrates. DNAmoreDB is a comprehensive database resource for DNAzymes that collects and organizes the following types of information: sequences, conditions of the selection procedure, catalyzed reactions, kinetic parameters, substrates, cofactors, structural information whenever available, and literature references. Currently, DNAmoreDB contains information about DNAzymes that catalyze 20 different reactions. We included a submission form for new data, a REST-based API system that allows users to retrieve the database contents in a machine-readable format, and keyword and BLASTN search features. The database is publicly available at https://www.genesilico.pl/DNAmoreDB/.

Recent Advances in Constructing Higher‐Order DNA Structures

“…DNAmoreDB (https://www.genesilico.pl/DNA-moreDB/) collects and organizes sequence and structural information, catalytic reaction conditions, kinetic parameters, substrates, cofactors, and literature references about DNAzymes. [15] Recently, Fe 3 + -assisted DNA nanoparticles (FeÀ DNA NPs) was synthesized by Li's group (Figure 1e) . [16] This simple and ingenious method enables the large-scale preparation of FeÀ DNA NPs by reacting DNA molecules with metal ions in one step at a suitable temperature.…”

Beyond the double helix: DNA structural diversity and the PDB

“…8 ). The first one identified ( 88 ) is able to bind to and catalytically cleave RNA sequences, and the large number (over 1500 ( 89 , 90 )) that have been subsequently found display a range of other catalytic activities as well, including not only the expected RNA ligation and DNA hydrolysis but can also catalyze a range of organic chemistry reactions—Diels-Alder, phosphorylation, and glycolysis to name just a few. Metals can be involved in the various catalytic mechanisms but are not universally required.…”

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

“…In the same area, 3DIV ( 19 ) reports an update focusing largely on 3D cancer genomes and commenting on the consequences for chromatin structure of the DNA structural variations associated with some cancers. Finally, DNAmoreDB ( 20 ) collects data on catalytic DNA molecules or DNAzymes, already demonstrated to catalyse 20 different reactions with that number sure to grow as research on their practical applications continues.…”