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Design of artificial nucleases and studies of their interaction with DNA

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Abstract

The design of artificial nucleases and nuclease mimics has attracted extensive attention and made great progress due to their significant scientific meanings and potential application in the field of gene medicine and molecular biology. This paper reviews recent progress in the investigation of artificial nuclease, including “bifunctional cooperative catalysis”, “dinuclear synergistic catalysis”, “metal-free catalysis”, and especially, the studies of aza-crown ethers as artificial nucleases and their interaction with DNA.

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References

  1. Sjoblom T, Jones S, Wood L D, Parsons D W, Lin J, Barber T D, Mandelker D, Leary R J, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz S D, Willis J, Dawson D, Willson J K V, Gazdar A F, Hartigan J, Wu L, Liu C S, Parmigiani G, Park B H, Bachman K E, Papadopoulos N, Vogelstein B, Kinzler K W, Vel-culescu V E. The consensus coding sequences of human breast and colorectal cancers. Science, 2006, 314(5797): 268–274

    Article  Google Scholar 

  2. Greenman C, Stephens P, Smith R, Dalgliesh G L, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O’Meara S, Vastrik I, Schmidt E E, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill D P, Louis D N, Goldstraw P, Nicholson A G, Brasseur F, Looijenga L, Weber B L, Chiew Y E, DeFazio A, Greaves M F, Green A R, Campbell P, Birney E, Easton D F, Chenevix-Trench G, Tan M H, Khoo S K, Teh B T, Yuen S T, Leung S Y, Wooster R, Futreal P A, Stratton M R. Patterns of somatic mutation in human cancer ge-nomes. Nature, 2007, 446(7132): 153–158

    Article  CAS  Google Scholar 

  3. Neidle S, Thurston D E. Chemical approaches to the discovery and development of cancer therapies. Nature Rev, 2005, 5(4): 285–296.

    Article  CAS  Google Scholar 

  4. Erkkila K E, Odom D T, Barton J K. Recognition and reaction of metallointercalators with DNA. Chem Rev, 1999, 99(9): 2777–2795

    Article  CAS  Google Scholar 

  5. Noll D M, McGregor M T, Miller P S. Formation and repair of inter-strand cross-links in DNA. Chem Rev, 2006, 106(2): 277–301

    Article  CAS  Google Scholar 

  6. Mancin F, Tecilla P. Zinc (II) complexes as hydrolytic catalysts of phosphate diester cleavage: From model substrates to nucleic acids. New J Chem, 2007, 31(6): 800–817

    Article  CAS  Google Scholar 

  7. Yuan C X, Yang P. Progress in metal complex conjugated to an oli-godeoxyribonucleotide as selective cleavage reagent. Prog Chem (in Chinese), 2005, 17(1): 80–86

    Google Scholar 

  8. Zhou L H, Wang N, Yu X Q. The interaction of macrocyclic poly-amine derivatives and their complexes with DNA. Prog Chem (in Chinese), 2007, 19(12): 74–83

    Google Scholar 

  9. Boerner L J K, Zaleski J M. Metal complex-DNA interactions: From transcription inhibition to photoactivated cleavage. Curr Opin Chem Biol, 2005, 9(2): 135–144

    Article  CAS  Google Scholar 

  10. Franklin S J. Lanthanide-mediated DNA hydrolysis. Curr Opin Chem Biol, 2001, 5(2): 201–208

    Article  CAS  Google Scholar 

  11. Cotton F A, Hazen E E J, Legg M J. Staphylococcal nuclease: Proposed mechanism of action based on structure of en-zyme-thymidine 3′,5′-bisphosphate-calcium ion complex at 1.5-.ANG. resolution. Proc Natl Acad Sci USA, 1979, 76(6): 2551–2555

    Article  CAS  Google Scholar 

  12. Weber D J, Meeker A K, Mildvan A S. Interactions of the acid and base catalysts on staphylococcal nuclease as studied in a double mutant. Biochemistry, 1991, 30(25): 6103–6114

    Article  CAS  Google Scholar 

  13. Jubian V, Dixon R P, Hamilton A D. Molecular recognition and catalysis. Acceleration of phosphodiester cleavage by a simple hydrogen-bonding receptor. J Am Chem Soc, 1992, 114(3): 1120–1121.

    CAS  Google Scholar 

  14. Dixon R P, Geib S J, Hamilton A D. Molecular recognition: Bis-acylguanidiniums provide a simple family of receptors for phosphodiesters. J Am Chem Soc, 1992, 114(1): 365–366

    Article  CAS  Google Scholar 

  15. Jubian V, Veronese A, Dixon R P, Hamilton A D. Acceleration of a phosphate diester transesterification reaction by bis (alkylguanidinium) receptors containing an appended general base. Angew Chem Int Ed Engl, 1995, 34(11): 1237–1239

    Article  CAS  Google Scholar 

  16. Muche M-S, Göebel M W. Bis(guanidinium) alcohols as models of staphylococcal nuclease: Substrate binding through ion pair complexes and fast phosphoryl transfer reactions. Angew Chem Int Ed Engl, 1996, 35(18): 2126–2129

    Article  CAS  Google Scholar 

  17. Ariga K, Anslyn E V. Manipulating the stoichiometry and strength of phosphodiester binding to a bisguanidine cleft in DMSO/water solutions. J Org Chem, 1992, 57(2): 417–419

    Article  CAS  Google Scholar 

  18. Smith J, Ariga K, Anslyn E V. Enhanced imidazole-catalyzed RNA cleavage induced by a bis-alkylguanidinium receptor. J Am Chem Soc, 1993, 115(1): 362–364

    Article  CAS  Google Scholar 

  19. Williams N H, Takasaki B, Wall M, Chin J. Structure and nuclease activity of simple dinuclear metal complexes: Quantitative dissection of the role of metal ions. Acc Chem Res, 1999, 32(6): 485–493

    Article  CAS  Google Scholar 

  20. Sigman D S, Mazumder A, Perrin D M. Chemical nucleases. Chem Rev, 1993, 93(6): 2295–2316

    Article  CAS  Google Scholar 

  21. Kövárí E, Krämer R. Rapid phosphodiester hydrolysis by an ammonium-functionalized copper (II) complex. A model for the cooperativity of metal ions and NH-acidic groups in phosphoryl transfer enzymes. J Am Chem Soc, 1996, 118(50): 12704–12709

    Article  Google Scholar 

  22. Kövári E, Heitker J, Krämer R. Metal-ammonium cooperativity in phosphodiester hydrolysis. J Chem Soc, Chem Commun, 1995, (12): 1205–1206

  23. Ait-Haddou H, Sumaoka J, Wiskur S L, Folmer-Andersen J F, Anslyn E V. Remarkable cooperativity between a Zn. ion and gua-nidinium/ammonium groups in the hydrolysis of RNA. Angew Chem Int Ed Engl, 2002, 41(21): 4013–4016

    Google Scholar 

  24. Feng G Q, Mareque-Rivas J C, Martin de Rosales R T, Williams N H. A highly reactive mononuclear Zn (II) complex for phosphodiester cleavage. J Am Chem Soc, 2005, 127(39): 13470–13471

    Article  CAS  Google Scholar 

  25. Feng G Q, Mareque-Rivas J C, Williams N H. Comparing a mono-nuclear Zn (II) complex with hydrogen bond donors with a dinuclear Zn (II) complex for catalyzing phosphate ester cleavage. Chem Commun, 2006, (17): 1845–1847

    Article  Google Scholar 

  26. Chen X Q, Wang J Y, Sun S G, Fan J L, Wu S, Liu J F, Ma S J, Zhang L Z, Peng X J. Efficient enhancement of DNA cleavage activity by introducing guanidinium groups into diiron (II) complex. Bioorg Med Chem Lett, 2008, 18(1): 109–113

    Article  CAS  Google Scholar 

  27. He J, Hu P, Wang Y J, Tong M L, Sun H Z, Mao Z W, Ji, L N. Double-strand DNA cleavage by copper complexes of 2,2′-dipyridyl with guanidinium/ammonium pendants. Dalton Trans, 2008, (24): 3207–3214

    Article  Google Scholar 

  28. An Y, Tong M L, Ji L N, Mao Z W. Double-strand DNA cleavage by copper complexes of 2,2′-dipyridyl with electropositive pendants. Dalton Trans, 2006, (17): 2066–2071

    Article  Google Scholar 

  29. Sheng X, Lu X M, Chen Y T, Lu G Y, Zhang J J, Shao Y, Liu F, Xu Q. Synthesis, DNA-binding, cleavage, and cytotoxic activity of new 1,7-dioxa-4,10-diazacyclododecane artificial receptors containing bisguanidinoethyl or diaminoethyl double side arms. Chem Eur J, 2007, 13(34): 9703–9712

    Article  CAS  Google Scholar 

  30. Shao Y, Sheng X, Li Y, Jia Z L, Zhang J J, Liu F, Lu G Y. DNA binding and cleaving activity of the new cleft molecule N,N′-bis (guanidinoethyl)-2,6-pyridinedicarboxamide in the absence or in the presence of copper (II). Bioconjugate Chem, 2008, 19(9): 1840–1848

    Article  CAS  Google Scholar 

  31. Ragunathan K G, Schneider H J. Binuclear lanthanide complexes as catalysts for the hydrolysis of bis(p-nitrophenyl) phosphate and double-stranded DNA. Angew Chem Int Ed Engl, 1996, 35(11): 1219–1221

    Article  CAS  Google Scholar 

  32. Zhao Y M, Zhu J H, He W J, Yang Z, Zhu Y G, Li Y Z, Zhang J F, Guo Z J. Oxidative DNA cleavage promoted by multinuclear copper complexes: Activity dependence on the complex structure. Chem Eur J, 2006, 12(25): 6621–6629

    Article  CAS  Google Scholar 

  33. Young M J, Chin J. Dinuclear copper (II) complex that hydrolyzes RNA. J Am Chem Soc, 1995, 117(42): 10577–10578

    Article  CAS  Google Scholar 

  34. Li Y, Lu X M, Sheng X, Lu G Y, Shao Y, Xu Q. DNA cleavage promoted by Cu 2+ complex of cyclen containing pyridine subunit. J Incl Phenom Macrocycl Chem, 2007, 59(1–2): 91–98

    Article  CAS  Google Scholar 

  35. Iranzo O, Elmer T, Richard J P, Morrow J R. Cooperativity between metal ions in the cleavage of phosphate diesters and RNA by dinuclear Zn (II) catalysts. Inorg Chem, 2003, 42(24): 7737–7746

    Article  CAS  Google Scholar 

  36. Xiang Q X, Zhang J, Liu P Y, Xia C Q, Zhou Z Y, Xie R G, Yu X Q. Dinuclear macrocyclic polyamine zinc (II) complexes: Syntheses, characterization and their interaction with plasmid DNA. J Inorg Biochem, 2005, 99(8): 1661–1669

    Article  CAS  Google Scholar 

  37. Sissi C, Rossi P, Felluga F, Formaggio F, Palumbo M, Tecilla P, Toniolo C, Scrimin P. Dinuclear Zn 2+ complexes of synthetic heptapeptides as artificial nucleases. J Am Chem Soc, 2001, 123(13): 3169–3170

    Article  CAS  Google Scholar 

  38. Sheng X, Guo X, Lu X M, Lu G Y, Shao Y, Liu F, Xu Q. DNA binding, cleavage, and cytotoxic activity of the preorganized dinuclear Zinc (II) complex of triazacyclononane derivatives. Bioconjugate Chem, 2008, 19(2): 490–498

    Article  CAS  Google Scholar 

  39. Anslyn E, Breslow R. Geometric evidence on the ribonuclease model mechanism. J Am Chem Soc, 1989, 111(15): 5972–5973

    Article  CAS  Google Scholar 

  40. Breslow R. Bifunctional acid-base catalysis by imidazole groups in enzyme mimics. J Mol Catal, 1994, 91(2): 161–174

    Article  CAS  Google Scholar 

  41. Wan S H, Liang F, Xiong X Q, Yang L, Wu X J, Wang P, Zhou X, Wu C T. DNA hydrolysis promoted by 1,7-dimethyl-1,4,7,10-tetraazacyclododecane. Bioorg Med Chem Lett, 2006, 16(10): 2804–2806

    Article  CAS  Google Scholar 

  42. Du J T, Li Y M, Wei W, Wu G S, Zhao Y F, Kanazawa K, Nemoto T, Nakanishi H. Low-barrier hydrogen bond between phosphate and the amide group in phosphopeptide. J Am Chem Soc, 2005, 127(47): 16350–16351

    Article  CAS  Google Scholar 

  43. Scheffer U, Strick A, Ludwig V, Peter S, Kalden E, Göebel Ml W. Metal-free catalysts for the hydrolysis of RNA derived from guanidines, 2-aminopyridines, and 2-aminobenzimidazoles. J Am Chem Soc, 2005, 127(7): 2211–2217

    Article  CAS  Google Scholar 

  44. Gnaccarini C, Peter S, Scheffer U, Vonhoff S, Klussmann S, Göebel M W. Site-specific cleavage of RNA by a metal-free artificial nuclease attached to antisense oligonucleotides. J Am Chem Soc, 2006, 128(24): 8063–8067

    Article  CAS  Google Scholar 

  45. Sheng X, Lu X M, Zhang J J, Chen Y T, Lu G Y, Shao Y, Liu F, Xu Q. Synthesis and DNA cleavage activity of artificial receptor 1,4,7-triazacyclononane containing guanidinoethyl and hydroxyethyl side arms. J Org Chem, 2007, 72(5): 1799–1802

    Article  CAS  Google Scholar 

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Correspondence to GuoYuan Lu.

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Supported by the National Natural Science Foundation of China (Grant Nos. 20872061 & 20372032) and the National Basic Research of China (Grant No. 2007CB925103)

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Zhang, J., Shao, Y., Wei, L. et al. Design of artificial nucleases and studies of their interaction with DNA. Sci. China Ser. B-Chem. 52, 402–414 (2009). https://doi.org/10.1007/s11426-009-0029-8

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  • DOI: https://doi.org/10.1007/s11426-009-0029-8

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