title: Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics.
abstract: Ezrin, a membrane organizer and linker between plasma membrane and cytoskeleton, is well documented to play an important role in the metastatic capacity of cancer cells especially for osteosarcoma cells. It has provided an ideal target for cancer gene therapy. RNA-cleaving 10-23 DNAzymes, consisting of a 15-nucleotide catalytical domain flanked by two target-specific complementary arms, can cleave the target mRNA at purine-pyrimidine dinucleotide effectively. In the present study, we designed and screened the target sites for 10-23 DNAzymes against ezrin mRNA by using multiple computational methods with combination of secondary structural and hybridization thermodynamic parameters. Then, we testified the activities of the DNAzymes directed against these selected target sites in vitro. Our results show that AU1751 is the most effective target site of ezrin mRNA for DNAzymes because of its ideal secondary structure and hybridization thermodynamics. So, there is a significant correlation between the multiple computational methods and the efficacy of the corresponding DNAzymes. These provide a rational, efficient way for DNAzymes selection.
authors.affiliation: Department of Orthopaedic Surgery, Musculoskeletal Tumor Center, The First Affiliated Hospital of Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, Guangdong, 510080, China.
authors.forename: YaoFei
authors.initials: Y
authors.lastname: Wang
authors.forename: JingNan
authors.initials: J
authors.lastname: Shen
authors.forename: XiFu
authors.initials: X
authors.lastname: Shang
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.forename: JingChun
authors.initials: J
authors.lastname: Li
authors.forename: JunQiang
authors.initials: J
authors.lastname: Yin
authors.forename: ChangYe
authors.initials: C
authors.lastname: Zou
mesh_terms: D000465:Algorithms; D003598:Cytoskeletal Proteins / Q000737:chemistry* / Q000235:genetics; D021881:DNA, Catalytic / Q000138:chemical synthesis*; D004277:DNA, Single-Stranded / Q000138:chemical synthesis*; D006801:Humans; D017403:In Situ Hybridization / Q000379:methods*; D017433:Protein Structure, Secondary; D012333:RNA, Messenger / Q000235:genetics; D013379:Substrate Specificity; D013816:Thermodynamics; D000099149:Ezrin
chemical_list: D003598:Cytoskeletal Proteins; D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; D012333:RNA, Messenger; D000099149:Ezrin; C402582:RNA-cleaving DNA 10-23