Bioinformatics Designing of 10-23 Deoxyribozyme against Coding Region of Beta-galactosidase Gene

Abstract

Background: Deoxyribozymes (Dzs) can play a role as gene expression inhibitors at mRNA level. Among Dzs, the 10-23 deoxyribozyme has significant potentials for treatment of diseases. Designed Dz includes a catalytic core made of 15 deoxyribonucleotides and two binding arms consisted of 6-12 nucleotides for site specific binding to target RNA and hydrolysis. The enzyme has characteristic features for cleavage of the RNA target between an unpaired purine (A, G) and a paired pyrimidine (C or U). In this study, 10-23 Dz is designed for the coding region of the α-peptide of a lacZ gene. Materials and Methods:The primary sequence of a plasmid with α-complementation ability was taken from addgene database. To confirm sequence validity, ExPASy was used to analyze related ORFs for the retrieved sequence. The ORF with identical sequence to α-peptide was selected in the reverse complement sequence. Subsequently, the secondary structure of the α-peptide was analyzed in DINAMelt web server and Mfold software. Then the intended target site was selected inside the coding region of the α-peptide. The Dzs sequence was designed for the target site with nucleotide binding arms. Results and conclusion:The resulted Dz in this study can be used as a promising catalytic DNA inside bacterial cells for blue-white screening. Criteria such as biological stability and catalytic rate of such enzymes must be evaluated in vivo and in vitro.

Specificity of oligonucleotide gene therapy (OGT) agents

“…When developing therapeutic Dz agents, researchers usually use the rules described in the pioneering work of Santoro and Joyce [142]. More recent work by Ahmadi et al contains a detailed explanation of the design of a Dz against a bacterial β-galactosidase gene using bioinformatics tools [158]. Even though the results of the developed Dz activity were not presented, the described approach might become useful in designing therapeutic Dz agents.…”