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Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics

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Tumor Biology

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.

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Acknowledgments

This work was supported by Research Fund for the Doctoral Program of Higher Education of China (20060558018). We thank Dr. PingXian Tan and Dr. BiCheng Yong at the Department of Orthopaedic Surgery, Musculoskeletal Tumor Center, the First Affiliated Hospital of Sun Yat-Sen University, for helpful discussions, comments, and critical reading of the manuscript.

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Authors and Affiliations

  1. 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

    YaoFei Wang, JingNan Shen, Jin Wang, JingChun Li, JunQiang Yin & ChangYe Zou

  2. Department of Orthopedic Surgery, Anhui Provincial Hospital, No.17 Lujiang Road, Hefei, China, 230001

    YaoFei Wang & XiFu Shang

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  1. YaoFei Wang
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  4. Jin Wang
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Correspondence to JingNan Shen.

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Wang, Y., Shen, J., Shang, X. et al. Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics. Tumor Biol. 32, 809–817 (2011). https://doi.org/10.1007/s13277-011-0183-4

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