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.
Similar content being viewed by others
References
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
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
Neidle S, Thurston D E. Chemical approaches to the discovery and development of cancer therapies. Nature Rev, 2005, 5(4): 285–296.
Erkkila K E, Odom D T, Barton J K. Recognition and reaction of metallointercalators with DNA. Chem Rev, 1999, 99(9): 2777–2795
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
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
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
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
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
Franklin S J. Lanthanide-mediated DNA hydrolysis. Curr Opin Chem Biol, 2001, 5(2): 201–208
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
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
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.
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
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
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
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
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
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
Sigman D S, Mazumder A, Perrin D M. Chemical nucleases. Chem Rev, 1993, 93(6): 2295–2316
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
Kövári E, Heitker J, Krämer R. Metal-ammonium cooperativity in phosphodiester hydrolysis. J Chem Soc, Chem Commun, 1995, (12): 1205–1206
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
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
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
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
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
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
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
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
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
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
Young M J, Chin J. Dinuclear copper (II) complex that hydrolyzes RNA. J Am Chem Soc, 1995, 117(42): 10577–10578
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
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
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
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
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
Anslyn E, Breslow R. Geometric evidence on the ribonuclease model mechanism. J Am Chem Soc, 1989, 111(15): 5972–5973
Breslow R. Bifunctional acid-base catalysis by imidazole groups in enzyme mimics. J Mol Catal, 1994, 91(2): 161–174
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
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
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
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
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
Author information
Authors and Affiliations
Corresponding author
Additional information
Supported by the National Natural Science Foundation of China (Grant Nos. 20872061 & 20372032) and the National Basic Research of China (Grant No. 2007CB925103)
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11426-009-0029-8