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

Author:

Mohammadi-Arani Razieh1,Javadi-Zarnaghi Fatemeh1,Boccaletto Pietro2ORCID,Bujnicki Janusz M2,Ponce-Salvatierra Almudena2ORCID

Affiliation:

1. Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan , Azadi Square, Hezar Jerib Avenue , 8174673441, Isfahan, Iran

2. Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw , ul. Ks. Trojdena 4, PL-02-109 Warsaw , Poland

Abstract

Abstract Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.

Funder

National Science Centre, Poland

University of Isfahan

Publisher

Oxford University Press (OUP)

Subject

Genetics

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