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Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme

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Abstract

HIV Integrase (IN) is an enzyme that is responsible for the integration of the proviral genome into the human genome, and this integration step is the first step of the virus hijacking the human cell machinery for its propagation and replication. 10-23 DNAzyme has the potential to suppress gene expressions through sequence-specific mRNA cleavage. We have designed three novel DNAzymes, DIN54, DIN116, and DIN152, against HIV-1 Integrase gene using Mfold software and evaluated them for target site cleavage activity on the in vitro transcribed mRNA. All DNAzymes were tested for its inhibition of expression of HIV Integrase protein in the transiently transfected cell lines. DIN116 and DIN152 inhibited IN-EGFP expression by 80% and 70% respectively.

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References

  • Achenbach JC, Chiuman W, Cruz RP and Li Y 2004 DNAzymes: from creation in vitro to application in vivo. Curr. Pharm. Biotechnol. 5 321–336

    Article  PubMed  CAS  Google Scholar 

  • Beger C, Pierce LN, Kruger M, Marcusson EG, Robbins JM, Welcsh P, Welch PJ, Welte K, et al. 2001 Identification of Id4 as a regulator of BRCA1 expression by using a ribozyme-library-based inverse genomics approach. Proc. Natl. Acad. Sci. USA 98 130–135

    Article  PubMed  CAS  Google Scholar 

  • Breaker RR and Joyce GF 1994 ADNA enzyme that cleaves RNA. Chem. Biol. 1 223–229

    Article  PubMed  CAS  Google Scholar 

  • Cairns MJ and Sun LQ 2004 Target-site selection for the 10–23 DNAzyme. Methods Mol. Biol. 252 267–277

    PubMed  CAS  Google Scholar 

  • Cao M, Ren H, Pan X, Pan W and Qi ZT 2004 Inhibition of EGFP expression by siRNA in EGFP-stably expressing Huh-7 cells. J. Virol. Methods 119 189–194

    Article  PubMed  CAS  Google Scholar 

  • Chan CW and Khachigian LM 2009 DNAzymes and their therapeutic possibilities. Intern. Med. J. 39 249–251

    Article  PubMed  CAS  Google Scholar 

  • Chandrasekhar K and Malathhi R 2003 Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes – a comparative study of group-I intron structures. J. Biosci. 28 547–555

    Article  PubMed  CAS  Google Scholar 

  • Dash BC and Banerjea AC 2004 Sequence-specific cleavage activities of DNA enzymes targeted against HIV-1 Gag and Nef regions. Oligonucleotides. 14 41–47

    Article  PubMed  CAS  Google Scholar 

  • Evering TH and Markowitz M 2008 Raltegravir: an integrase inhibitor for HIV-1. Expert Opin. Investig. Drugs 17 413–422

    Article  PubMed  CAS  Google Scholar 

  • Goila R and Banerjea AC 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

    Article  PubMed  CAS  Google Scholar 

  • Goodchild J 2004 Oligonucleotide therapeutics: 25 years agrowing. Curr. Opin. Mol. Ther. 6 120–128

    PubMed  CAS  Google Scholar 

  • Gupta SP and Nagappa AN 2003 Design and development of integrase inhibitors as anti-HIV agents. Curr. Med. Chem. 10 1779–1794

    Article  PubMed  CAS  Google Scholar 

  • Hou W, Ni Q, Wo J, Li M, Liu K, Chen L, Hu Z, Liu R and Hu M 2006 Inhibition of hepatitis B virus X gene expression by 10–23 DNAzymes. Antiviral Res. 72 190–196

    Article  PubMed  CAS  Google Scholar 

  • Joyce GF 2001 RNA cleavage by the 10–23 DNA enzyme. Methods Enzymol. 341 503–517

    Article  PubMed  CAS  Google Scholar 

  • Joyce GF 2004 Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73 791–836

    Article  PubMed  CAS  Google Scholar 

  • Kurreck J, Wyszko E, Gillen C and Erdmann VA 2002 Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 30 1911–1918

    Article  PubMed  CAS  Google Scholar 

  • Lu ZX, Ye M, Yan GR, Li Q, Tang M, Lee LM, Sun LQ and Cao Y 2005 Effect of EBVLMP1 targeted DNAzymes on cell proliferation and apoptosis. Cancer Gene Ther. 12 647–654

    Article  PubMed  CAS  Google Scholar 

  • Mathews DH, Sabina J, Zuker M and Turner DH 1999 Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 911–940

    Article  PubMed  CAS  Google Scholar 

  • Mitchell A, Dass CR, Sun LQ and Khachigian LM 2004 Inhibition of human breast carcinoma proliferation, migration, chemoinvasion and solid tumour growth by DNAzymes targeting the zinc finger transcription factor EGR-1. Nucleic Acids Res. 32 3065–3069

    Article  PubMed  CAS  Google Scholar 

  • Nagy P, Arndt-Jovin DJ and Jovin TM 2003 Small interfering RNAs suppress the expression of endogenous and GFP-fused epidermal growth factor receptor (erbB1) and induce apoptosis in erbB1-overexpressing cells. Exp. Cell Res. 285 39–49

    Article  PubMed  CAS  Google Scholar 

  • Ota N, Warashina M, Hirano K, Hatanaka K and Taira K 1998 Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity. Nucleic Acids Res. 26 3385–3391

    Article  PubMed  CAS  Google Scholar 

  • Passman M, Weinberg M, Kew M and Arbuthnot P 2000 In situ demonstration of inhibitory effects of hammerhead ribozymes that are targeted to the hepatitis Bx sequence in cultured cells. Biochem. Biophys. Res. Commun. 268 728–733

    Article  PubMed  CAS  Google Scholar 

  • Peracchi A 2004 Prospects for antiviral ribozymes and deoxyribozymes. Rev. Med. Virol. 14 47–64

    Article  PubMed  CAS  Google Scholar 

  • Qin ZL, Zhao P, Zhang XL, Yu JG, Cao MM, Zhao LJ, Luan J and Qi ZT 2004 Silencing of SARS-CoV spike gene by small interfering RNA in HEK 293 T cells. Biochem. Biophys. Res. Commun. 324 1186–1193

    Article  PubMed  CAS  Google Scholar 

  • Reeder J, Hochsmann M, Rehmsmeier M, Voss B and Giegerich R 2006 Beyond Mfold: recent advances in RNA bioinformatics. J. Biotechnol. 124 41–55

    Article  PubMed  CAS  Google Scholar 

  • Roy S, Gupta N, Subramanian N, Mondal T, Banerjea AC and Das S 2008 Sequence-specific cleavage of hepatitis C virus RNA by DNAzymes: inhibition of viral RNA translation and replication. J. Gen. Virol. 89 1579–1586

    Article  PubMed  CAS  Google Scholar 

  • Santoro SW and Joyce GF 1997 A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94 4262–4266

    Article  PubMed  CAS  Google Scholar 

  • Saxena V and Dhole TN 2008 Preventive strategies for frequent outbreaks of Japanese encephalitis in Northern India. J. Biosci. 33 505–514

    Article  PubMed  Google Scholar 

  • Schubert S and Kurreck J 2004 Ribozyme- and deoxyribozyme-strategies for medical applications. Curr. Drug Targets 5 667–681

    Article  PubMed  CAS  Google Scholar 

  • Silverman SK 2004 Breaking up is easy to do (if you're a DNA enzyme that cleaves RNA). Chem. Biol. 11 7–8

    PubMed  CAS  Google Scholar 

  • Silverman SK 2005 In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res. 33 6151–6163

    Article  PubMed  CAS  Google Scholar 

  • Unwalla H and Banerjea AC 2001 Novel mono- and di-DNA-enzymes targeted to cleave TAT or TAT-REVRNA inhibit HIV-1 gene expression. Antiviral Res. 51 127–139

    Article  PubMed  CAS  Google Scholar 

  • Unwalla H, Chakraborti S, Sood V, Gupta N and Banerjea AC 2006 Potent inhibition of HIV-1 gene expression and TAT-mediated apoptosis in human T cells by novel mono- and multitarget anti-TAT/Rev/Env ribozymes and a general purpose RNA-cleaving DNA-enzyme. Antiviral Res. 72 134–144

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Shen J, Shang X, Wang J, Li J, Yin J and Zou C 2011 Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics. Tumour Biol. 32 809–817

    Article  PubMed  CAS  Google Scholar 

  • Warashina M, Kuwabara T, Nakamatsu Y and Taira K 1999 Extremely high and specific activity of DNA enzymes in cells with a Philadelphia chromosome. Chem. Biol. 6 237–250

    Article  PubMed  CAS  Google Scholar 

  • Wu Y, Yu L, McMahon R, Rossi JJ, Forman SJ and Snyder DS 1999 Inhibition of bcr-abl oncogene expression by novel deoxyribozymes (DNAzymes). Hum. Gene Ther. 10 2847–2857

    Article  PubMed  CAS  Google Scholar 

  • Xie YY, Zhao XD, Jiang LP, Liu HL, Wang LJ, Fang P, Shen KL, Xie ZD, Wu YP and Yang XQ 2006 Inhibition of respiratory syncytial virus in cultured cells by nucleocapsid gene targeted deoxyribozyme (DNAzyme). Antiviral Res. 71 31–41

    Article  PubMed  CAS  Google Scholar 

  • Zaborowska Z, Schubert S, Kurreck J and Erdmann VA 2005 Deletion analysis in the catalytic region of the 10–23 DNA enzyme. FEBS Lett. 579 554–558

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Zuker M 2003 Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 3406–3415

    Article  PubMed  CAS  Google Scholar 

  • Zuker M and Stiegler P 1981 Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9 133–148

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgement

NS and SS are grateful to University Grants Commission (UGC), India, for the Senior Research Fellowship. AR is grateful to Council of Scientific & Industrial Research (CSIR). This work was funded by the grant obtained from UGC and Department of Science and Technology (DST), India.

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Authors and Affiliations

  1. Dr BR Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, 110 007, India

    Nirpendra Singh & Ramesh Chandra

  2. Department of Chemistry, University of Delhi, New Delhi, 110 007, India

    Atul Ranjan, Souvik Sur & Vibha Tandon

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  1. Nirpendra Singh
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  2. Atul Ranjan
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  3. Souvik Sur
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  4. Ramesh Chandra
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  5. Vibha Tandon
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Corresponding author

Correspondence to Vibha Tandon.

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[Singh N, Ranjan A, Sur S, Chandra R and Tandon V 2012 Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme. J. Biosci. 37 1–10] DOI 10.1007/s12038-012-9216-4

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Singh, N., Ranjan, A., Sur, S. et al. Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme. J Biosci 37, 493–502 (2012). https://doi.org/10.1007/s12038-012-9216-4

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  • DOI: https://doi.org/10.1007/s12038-012-9216-4

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