Literature DB >> 33053178

DNAmoreDB, a database of DNAzymes.

Almudena Ponce-Salvatierra1, Pietro Boccaletto1, Janusz M Bujnicki1,2.   

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/.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33053178     DOI: 10.1093/nar/gkaa867

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  8 in total

1.  Programming a DNA tetrahedral nanomachine as an integrative tool for intracellular microRNA biosensing and stimulus-unlocked target regulation.

Authors:  Lianyu Yu; Sha Yang; Zeyu Liu; Xiaopei Qiu; Xiaoqi Tang; Shuang Zhao; Hanqing Xu; Mingxuan Gao; Jing Bao; Ligai Zhang; Dan Luo; Kai Chang; Ming Chen
Journal:  Mater Today Bio       Date:  2022-05-06

Review 2.  Biosensing with DNAzymes.

Authors:  Erin M McConnell; Ioana Cozma; Quanbing Mou; John D Brennan; Yi Lu; Yingfu Li
Journal:  Chem Soc Rev       Date:  2021-07-06       Impact factor: 60.615

3.  DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes.

Authors:  Razieh Mohammadi-Arani; Fatemeh Javadi-Zarnaghi; Pietro Boccaletto; Janusz M Bujnicki; Almudena Ponce-Salvatierra
Journal:  Nucleic Acids Res       Date:  2022-04-21       Impact factor: 19.160

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

Authors:  Daniel J Rigden; Xosé M Fernández
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

Review 5.  Beyond the double helix: DNA structural diversity and the PDB.

Authors:  Stephen Neidle
Journal:  J Biol Chem       Date:  2021-03-17       Impact factor: 5.157

6.  DNAzyme as a rising gene-silencing agent in theranostic settings.

Authors:  Nan Zhang
Journal:  Neural Regen Res       Date:  2022-09       Impact factor: 5.135

Review 7.  Revisiting the Extinction of the RNA World.

Authors:  Anthony C Forster
Journal:  Biochemistry       Date:  2022-04-07       Impact factor: 3.321

8.  CATANA: an online modelling environment for proteins and nucleic acid nanostructures.

Authors:  David Kuťák; Lucas Melo; Fabian Schroeder; Zoe Jelic-Matošević; Natalie Mutter; Branimir Bertoša; Ivan Barišić
Journal:  Nucleic Acids Res       Date:  2022-05-11       Impact factor: 19.160

  8 in total

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