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

Ahmadi, Nasrin al-Sadat and Esmaeili, Abolghasem and JavadiZarnaghi, Fatemeh (2017) Bioinformatics Designing of 10-23 Deoxyribozyme against Coding Region of Beta-galactosidase Gene. Research in Molecular Medicine, 5 (2). pp. 28-33.

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Official URL: http://rmm.mazums.ac.ir/article-1-240-en.html

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. Material 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.

Item Type: Article
Uncontrolled Keywords: 10-23 deoxyribozyme, gene expression, beta-galactosidase gene
Depositing User: Unnamed user with email eprints@mazums.ac.ir
Date Deposited: 04 Jan 2018 15:05
Last Modified: 04 Jan 2018 15:05
URI: http://eprints.mazums.ac.ir/id/eprint/1711

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