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

• Main Authors: Nasrin al-Sadat Ahmadi, Abolghasem Esmaeili, Fatemeh Javadi Zarnaghi
• Format: Article
• Language: English
• Published: Mazandaran University of Medical Sciences and Health Services 2017-05-01
• Series: Research in Molecular Medicine
• Subjects: 10-23 deoxyribozyme; gene expression; beta-galactosidase gene
• Online Access: http://rmm.mazums.ac.ir/browse.php?a_code=A-10-751-2&slc_lang=en&sid=1

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.