Abstract
The selective inactivation of a target gene by antisense mechanisms is an important biological tool in the delineation of gene functions. Ribozymes and RNA-cleaving DNA enzymes-mediated approaches are more attractive because of their ability to catalytically cleave the target RNA. DNA enzymes have recently gained great importance because they are short DNA molecules with simple structures that are expected to be stable to the nucleases present inside a mammalian cell. We have designed a strategy to identify accessible cleavage sites in human immunodeficiency virus-1 (HIV-1) gag RNA from a pool of random DNA enzymes, and for isolation of DNA enzymes. A pool of random sequences 29 nucleotides long that contained the previously identified 10–23 catalytic motif were tested for their ability to cleave the target RNA. When the pool of random DNA enzymes was targeted to cleave between A and U nucleotides, a DNA enzyme 1836 was identified. Although several DNA enzymes were identified using a pool of DNA enzyme that was completely randomized with respect to its substrate-binding properties, DNA enzyme-1810 was selected for further characterization. Both the DNA enzymes showed target-specific cleavage activities in the presence of Mg2+ only. These strategies could be applied for the selection of desired target sites in any target RNA.
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References
Santoro, S. W. and Joyce, G. F. (1997) A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94, 4262–4266.
Santiago, F. S., Lowe, H. C., Kavurma, M. M., Chesterman, C. N., Baker, A., Atkins, D. G., and Khachigian, L. M. (1999) New DNA enzyme targeting Egr-1 mRNA inhibits vascular smooth muscle proliferation and regrowth after injury. Nature Med. 11, 1264–1269.
Wu, Y., Yu, L., McMahon, R., Rossi, J. J., Forman, S. J., and Snyder, D. S. (1999) Inhibition of bcr-abl oncogene expression by novel deoxyribozymes (DNAzymes). Human Gene Ther. 10, 2847–2857.
Zhang, X., Xu, Y., Ling, H., and Hattori, T. (1999) Inhibition of infection of incoming HIV-1 virus by RNA-cleaving DNA enzyme. FEBS Lett. 458, 151–156.
Dash, B. C., Harikrishnan, T. A., Goila, R., Shahi, S., Unwalla, H., Husain, S., and Banerjea, A. C. (1998) Targeted cleavage of HIV-1 envelope gene by a DNA enzyme and inhibition of HIV-1 envelope-CD4 mediated cell fusion. FEBS Lett. 431, 395–399.
Goila, R. and Banerjea, A. C. (1998) Sequence specific cleavage of the HIV-1 coreceptor-CCR5 gene by a hammer-head ribozyme and a DNA enzyme: inhibition of the coreceptor function by DNA enzyme. FEBS Lett. 436, 233–238.
Basu, S., Sriram, B., Goila, R., and Banerjea, A. C. (2000) Targeted cleavage of HIV-1 coreceptor-CXCR-4 by RNA cleaving DNA enzyme: Inhibition of the coreceptor function by DNA enzyme. Antiviral Res. 46, 125–134.
Unwalla, H. and Banerjea, A. C. (2001) Novel mono-and di-DNA enzymes targeted to cleave TAT and TAT-REV RNA inhibit HIV-1 gene expression. Antiviral Res. 51, 127–139.
Adachi, A., Gendelman, H. E., Koenig, S., Folks, T., Willey, R., Rabson, A., and Martin, M. A. (1986) Production of acquired immunodeficiency syndrome associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. J. Virol. 59, 284–291.
Goila, R. and Banerjea, A. C. (2001) Inhibition of hepatitis B virus X gene expression by novel DNA enzymes. Biochem. J. 353, 701–708.
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© 2004 Humana Press Inc., Totowa, NJ
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Chakraborti, S., Sriram, B., Banerjea, A.C. (2004). In Vitro Selected RNA-Cleaving DNA Enzymes From Combinatorial Libraries. In: Sioud, M. (eds) Ribozymes and siRNA Protocols. Methods in Molecular Biology™, vol 252. Humana Press. https://doi.org/10.1385/1-59259-746-7:279
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DOI: https://doi.org/10.1385/1-59259-746-7:279
Publisher Name: Humana Press
Print ISBN: 978-1-58829-226-1
Online ISBN: 978-1-59259-746-8
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