Hairpin probe for sequence-specific recognition of double-stranded DNA on simian virus 40

Abstract

Simian virus 40(SV40) is a polyomavirus and can induce a series of different tumors. The recognition of SV40 genome is crucial to tumor diagnosis and gene therapy. Herein, a sensitive and selective colorimetric method for sequence-specific recognition of homopyrimidine·homopurine duplex DNA(dsDNA) of SV40(4424—4440, gp6) was established with a hairpin probe based upon the formation of triplex DNA. Hairpin probe 5′-CCC TAC CCA TTT TTT CTT CTC TTT CCT GGG TAG GGC GGG TTG GG-3′(HP) containing G-rich sequence and 17-bp trip-lex-forming sequence was used as the signal probe, which was stem-loop structure alone and exhibited low catalytic activity. Upon its binding to the target duplex of SV40, hairpin probe transferred from stem-loop structure to parallel triplex DNA, accompanied by the recovery of catalytic activity of DNAzyme and a sharp increase of absorbance. Under optimum conditions, the absorbance was increased proportionally to the concentration of dsDNA over the range from 500 pmol/L to 40.0 nmol/L with a detection limit of 433 pmol/L. Moreover, satisfied results were obtained when the assay was used to recognize the mismatched sequences.

Keywords

Simian virus 40 / Hairpin probe / Triplex DNA / G-Quadruplex DNAzyme

References

[1] Wang Z. J., Lee J. H., Lu Y. Adv. Mater., 2008, 20(17): 3263.

[2] Zhou W. J., Gong X., Xiang Y., Yuan R., Chai Y. Q. Biosens. Bioelectron., 2014, 55: 220.

[3] Lin Z. Y., Yang W. Q., Zhang G. Y., Liu Q. D., Qiu B., Cai Z. W., Chen G. N. Chem. Commun, 2011, 47(32): 9069.

[4] Wang S. R., Fu B. S., Peng S., Zhang X. E., Tian T., Zhou X. Chem. Commum., 2013, 49(72): 7920.

[5] Zhou X. H., Kong D. M., Shen H. X. Anal. Chem., 2010, 82(3): 789.

[6] Li T., Wang E. K., Dong S. J. J. Am. Chem. Soc., 2009, 131(42): 15082.

[7] Wang X. P., Yin B. C., Wang P., Ye B. C. Biosens. Bioelectron., 2013, 42: 131.

[8] Huang Y., Chen J., Zhao S. L., Shi M., Chen Z. F., Liang H. Anal. Chem., 2013, 85(9): 4423.

[9] Li R. M., Xiong C., Xiao Z. Y., Ling L. S. Anal. Chim. Acta, 2012, 724: 80.

[10] Dylla-Spears R., Townsend J. E., Sohn L. L., Jen-Jacobson L., Muller S. J. Anal. Chem., 2009, 81(24): 10049.

[11] Rucker V. C., Foister S., Melander C., Dervan P. B. J. Am. Chem. Soc., 2003, 125(5): 1195.

[12] McKenzie F., Faulds K., Graham D. Chem. Commun., 2008, 28: 2367.

[13] Park K. S., Jung C., Park H. G. Angew. Chem., Int. Ed., 2010, 49(50): 9757.

[14] Singh I., Wendeln C., Clark A. W., Cooper J. M., Ravoo B. J., Burley G. A. J. Am. Chem. Soc., 2013, 135(9): 3449.

[15] Thompson M. Bioconjugate Chem., 2006, 17(2): 507.

[16] Roberts T. L., Idris A., Dunn J. A., Kelly G. M., Burnton C. M., Hodgson S., Hardy L. L., Garceau V., Sweet M. J., Ross I. L., Hume D. A., Stacey K. J. Science, 2009, 323(5917): 1057.

[17] Miao X. M., Guo X. T., Xiao Z. Y., Ling L. S. Biosens. Bioelectron., 2014, 59: 54.

[18] Wu C. K., Zhou Y. M., Miao X. M., Ling L. S. Analyst, 2011, 136(10): 2106.

[19] Ihara T., Ishii T., Araki N., Wilson A. W., Jyo A. J. Am. Chem. Soc., 2009, 131(11): 3826.

[20] Chan P. P., Glazer P. M. J. Mol. Med., 1997, 75(4): 267.

[21] Pelkmans L., Püntener D., Helenius A. Science, 2002, 296(5567): 535.

[22] Gazdar A. F., Butel J. S., Carbone M. Nat. Rev. Cancer, 2002, 2(12): 957.

[23] Foddis R., Rienzo A. D., Broccoli D., Bocchetta M., Stekala E., Riz-zo P., Tosolini A., Grobelny J. V., Jhanwar S. C., Pass H. I., Testa J. R., Carbone M. Oncogene, 2002, 21(9): 1434.

[24] Deeb K. K., Michalowska A. M., Yoon C. Y., Krummey S. M., Hoe-nerhoff M. J., Kavanaugh C., Li M. C., Demayo F. J., Linnoila I., Deng C. X., Lee E. Y.-H. P., Medina D., Shih J. H., Green J. E. Can-cer Res., 2007, 67(17): 8065.

[25] Ali S. H., DeCaprio J. A. Semin. Cancer Biol., 2001, 11(1): 15.

[26] Ahuja D., Sáenz-Robles M. T., Pipas J. M. Oncogene, 2005, 24: 7729.

[27] Tyagi S., Kramer F. R. Nat. Biotechnol., 1996, 14(3): 303.

[28] Xiao Z. Y., Guo X. T., Ling L. S. Chem. Commun., 2013, 49(34): 3573.

[29] Heyduk T., Heyduk E. Nat. Biotechnol., 2002, 20(2): 171.

[30] Kim B., Jung I. H., Kang M. J., Shim H. K., Woo H. Y. J. Am. Chem. Soc., 2012, 134(6): 3133.

[31] Xu H., Hepel M. Anal. Chem., 2011, 83(3): 813.

[32] Hu R., Liu Y. R., Zhang X. B., Tan W. H., Shen G. L., Yu R. Q. Bio-sens. Bioelectron., 2013, 41: 442.

[33] Tyagi S., Marras S. A., Kramer F. R. Nat. Biotechnol., 2000, 18(11): 1191.

[34] Tan W. H., Wang K., Drake T. J. Molecular Beacons. Curr. Opin. Chem. Biol., 2004, 8(5): 547.

[35] Fan C., Plaxco K. W., Heeger A. J. P. Natl. A. Sci. USA, 2003, 100(16): 9134.

[36] Xiao Y., Pavlov V., Iazov T., Dishon A., Kotler M., Willner I. J. Am. Chem. Soc., 2004, 126(24): 7430.

[37] Gao Y., Li B. X. Anal. Chem., 2013, 85(23): 11494.