Advertisement

Chinese Science Bulletin

, Volume 45, Issue 22, pp 2017–2028 | Cite as

Research progresses of artificial nucleic acid cleavage agents

  • Rong Wan
  • Gang Zhao
  • Jing Chen
  • Yufen Zhao
Review

Abstract

Artificial nucleic acid cleavage agents have attracted close attention because they play important roles in biochemistry and molecular biology. According to the cleavage mechanism of nucleic acid, they are divided into three types, namely free radical, phosphodiester bond hydrolysis and elimination cleavage agents. In this review, a series of cleavage agents, including the site- and sequence-specific ones, are illustrated, and some suggestions for the future researches in this field are also put forward.

Keywords

nucleic acid cleavage agents site- and sequence-specific cleavage agents free radical phosphodiester bond hydrolysis elimination 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Breslow, R., Bitunctional acid-base catalysis by imidazole groups in enzyme mimics, J. Molecular Catalysis, 1994, 91(2): 161.CrossRefGoogle Scholar
  2. 2.
    Crookc, S. T., Antisense oligonucleotides, Cancer Ther., 1997: 299.Google Scholar
  3. 3.
    Ausubel, F. M., Brent, R. (eds.). Current Protocols in Molecular Biology, New York: Green Publishing Associates and Wiley-Intersciencc, 1992.Google Scholar
  4. 4.
    Tullius, T. D., DNA footprinting with hydroxyl radical, Nature, 1988, 332(6165): 663.CrossRefGoogle Scholar
  5. 5.
    Muth, G. W., Thompson, C. M., Hill, W. E., Cleavage of a 23s rRNA pseudoknot by phenanthroline-Cu(II), Nucleic Acids Res., 1999, 27(8): 1906.CrossRefGoogle Scholar
  6. 6.
    Pogozelski, W. K., Tullius. T. D., Oxidative strand scission of nucleic acids: routes initiated by hydrogen abstraction from the sugar moiety, Chem. Rev., 1998(3): 1089.Google Scholar
  7. 7.
    Rokita, S. E., Romero-Fredes, L., The ensemble reactions of hydroxyl radical exhibit no specificity for primary or secondary structure of DNA. Nucleic Acids Res., 1992, 20(12): 3069.CrossRefGoogle Scholar
  8. 8.
    Tullius, T. D., Dombroski, B. A., Hydroxyl radical “foolprinling”: high-resolution information about DNA-protein contacts and application to λ rcpressor and cro protein, Proc. Nail. Acad. Sci. USA, 1986, 53(15): 5469.CrossRefGoogle Scholar
  9. 9.
    Sigman, D. S., Graham, D. R., D’Aurora, V. et al., Oxygen-dependent cleavage of DNA by the 1,10-phenanthroline cuprous complex, J. Biol. Chem., 1979, 254(24): 12269.Google Scholar
  10. 10.
    Kuwabara, M., Yoon, C., Goyne, T. et al., Nuclease activity of 1,10-phenanthroline-copper ion: reaction with CGCGAATTCGCG and its complexes with nelropsin and EcoRI, Biochemistry, 1986, 25(23): 7401.CrossRefGoogle Scholar
  11. 11.
    Murakawa, G. J., Chen, C. B., Kuwabara, M. D. et al., Scission of RNA by the chemical nuclease of 1,10-phenanthrolinecopper ion: preference for single-stranded loops. Nucleic Acids Res., 1989, 17(13): 5361.CrossRefGoogle Scholar
  12. 12.
    Mei, H. Y., Barton, J. K., Tris(telramethylphenanlhroline)ruthenium(II): a chrial proke that cleaves A-DNA conformations, Proc. Nail. Acad. Sci. USA, 1988, 85(5): 1339.CrossRefGoogle Scholar
  13. 13.
    Neyhart, G. A., Cheng, C. C., Thorp, H. H., Kinetics and mechanism of the oxidation of sugars and nucleotides by oxorulhenium(IV): model studies for predicting cleavage patterns in polymeric DNA and RNA, J. Am. Chem. Soc, 1995, 117(5): 1463.CrossRefGoogle Scholar
  14. 14.
    Sitilani, A., Long, E. C., DNA photocleavage by phenanthrenequinone diimine complexes of rhodium(III): shape-selective recognition and reaction, J. Am. Chem. Soc., 1992, 114(7): 2303.CrossRefGoogle Scholar
  15. 15.
    Mack, D. P., Iverson, B. L., Dervan, P. B., Design and chemical synthesis of a sequence-specific DNA-cleaving protein, J. Am. Chem. Soc., 1988, 110(22): 7572.CrossRefGoogle Scholar
  16. 16.
    Reed, C. J., Douglas, K. T., Single-slrand cleavage of DNA by Cu(II) and thiols: a powerful chemical DNA-cleaving system, Biochem. Biophys. Res. Commun., 1989, 162(3): 1111.CrossRefGoogle Scholar
  17. 17.
    John, D. C. A., Douglas, K. T., A common chemical mechanism used for DNA cleavage by copper(II) activated by thiols and ascorbate is distinct from that for copper(II): hydrogen peroxide cleavage. Transition Met. Chem., 1996, 21(5): 460.CrossRefGoogle Scholar
  18. 18.
    Ward, B., Skorobogaly, A., Dabrowiak, J. C., DNA cleavage specificity of a group of cationic metalloporphyrins. Biochemistry, 1986, 25(22): 6875.CrossRefGoogle Scholar
  19. 19.
    Nielsen, P. E., Jeppesen, C., Buchardt, O., Uranyl salts as photochemical agents for cleavage of DNA and probing of protein-DNA contacts, FEBS Lett., 1988, 235 (1, 2): 122.CrossRefGoogle Scholar
  20. 20.
    Carter, P. J., Breiner, K. M., Thorp, H. H., Effects of secondary structure on DNA and RNA cleavage by diplatinum(II), Biochemistry, 1998, 37(39): 13736.CrossRefGoogle Scholar
  21. 21.
    Bernstein, R., Prat, F., Foote, C. S., On the mechanism of DNA cleavage by fullerenes investigated in model systems: electron transfer from guanosine and 8-oxo-guanosine derivatives to C60, J. Am. Chem. Soc., 1999, 121(2): 464.CrossRefGoogle Scholar
  22. 22.
    Daniels, J. S., Chatterji, T., Macgillivrag, L. R. et al., Photochemical DNA cleavage by the antitumor agent 3-amino-l,2.4-benzotriazine 1,4-dioxide, J. Org. Chem., 1998, 63(26): 10027.CrossRefGoogle Scholar
  23. 23.
    Shimidzu, T., Oligonucleotides shackled with letraphenylporphyrin. Phosphorus Sulfur and Silicon, 1996, 110 (1–4): 269.Google Scholar
  24. 24.
    Lau, S. J., Kruck, T. P. A., Sarker, B., A peptide molecule mimicking the copper(II) transport site of human serum albumin, J. Biol. Chem., 1974, 249(18): 5878.Google Scholar
  25. 25.
    Inoue, S., Kawanishi, S., ESR evidence for Superoxide, hydroxyl radicals and singlet oxygen produced from hydrogen peroxide and nickeK (II) complex of glycylglycyl-1-histidine, Biochem. Biophys. Res. Commun., 1989, 159(2): 445.CrossRefGoogle Scholar
  26. 26.
    Huang, X. F., Pieczko, M. E., Long, E. C., Combinatorial optimization of the DNA cleaving Ni2+· Xaa-Xaa-his metallotripeptide domain, Biochemistry, 1999, 38(7): 2160.CrossRefGoogle Scholar
  27. 27.
    Brittain, I. J., Huang, X. F., Long, E. C., Selective recognition and cleavage of RNA loop structures by Ni(II) · Xau-gly-his metallopeptides. Biochemistry, 1998, 37(35): 12113.CrossRefGoogle Scholar
  28. 28.
    Freedman, J. H., Pickard, L., Weinstein, B. et al., Structure of the glycyl-1-histidyl-l-lysine-coppeit (II) complexes in solution, Biochemistry, 1982, 21(19): 4540.CrossRefGoogle Scholar
  29. 29.
    Bailly, C., Sun, J.-S., Footprinting studies on the sequence-selective binding of tilorone to DNA, Bioconjugate Chem., 1992, 3: 100.CrossRefGoogle Scholar
  30. 30.
    Burger, R. M., Cleavage of nucleic acids by bleomycin, Chem. Rev., 1998, 98(3): 1153.CrossRefGoogle Scholar
  31. 31.
    Boger, D. L., Cai, H., Bleomycin: synthetic and mechanistic studies, Angew. Chem. Int. Ed., 1999, 38(4): 448.CrossRefGoogle Scholar
  32. 32.
    Zeng, X. P., Xi, Z., Kappen, L. S. et al., Double-stranded damage of DNA-RNA hybrids by neocarzinostatin chromophore: selective c-1′ chemistry on the RNA strand. Biochemistry, 1995, 34(38): 12435.CrossRefGoogle Scholar
  33. 33.
    Podyminogin, M. A., Vlassov, V. V., Giege, R., Synthetic RNA-cleaving molecules mimicking ribonuclease an active center: design and cleavage of (RNA transcripts. Nucleic Acids Res., 1993, 21(25): 5950.CrossRefGoogle Scholar
  34. 34.
    Lorente, A., Espinosa, J. F., Fernandezsaiz, M. et al., Synthesis of imidazole-acridine conjugates as ribonuclease A mimics. Tetrahedron Letters. 1996, 37(25): 4417.CrossRefGoogle Scholar
  35. 35.
    Breslow, R., Labelle, M., Sequential general base-acid catalysis in the hydrolysis of RNA by imidazole, J. Am. Chem. Soc., 1986, 108(10): 2655.CrossRefGoogle Scholar
  36. 36.
    Konevetz, D. A., Beck, I. E., Artificial ribonucleases: synthesis and RNA cleaving properties of cationic conjugates bearing imidazole residues. Tetrahedron, 1999, 55(2): 503.CrossRefGoogle Scholar
  37. 37.
    Breslow, R., How do imidazole groups catalyze the cleavage of RNA in enzyme models and in enzymes? Evidence from “negative catalysis”, Acc. Chem. Res., 1991, 24(11): 317.CrossRefGoogle Scholar
  38. 38.
    Bruice, T. C., Tsubouchi, A., Dempcy, R. O. et al., One-metal and 2-metal ion catalysis of the hydrolysis of adenosine 3′ ’ alkyl phosphate-esters—models for one-metal and 2-metal ion catalysis of RNA hydrolysis, J. Am. Chem. Soc., 1996, 118(41): 9867.CrossRefGoogle Scholar
  39. 39.
    Chin, J., Developing artificial hydrolytic metalloenzymes by a unified mechanism approach, Acc. Chem. Res., 1991, 24(5): 145.CrossRefGoogle Scholar
  40. 40.
    Komiyama, M., Sumaoka, J., Yonezawa, K. et al., Structure-reactivity relationship for the cobalt(III) complex-catalysed hydrolysis of adenosine 3′, 5′cyclic monophosphate, J. Chem. Soc. Perkin Trans. 2, 1997 (1): 75.Google Scholar
  41. 41.
    Eichhorn, G. L., Marzilli, L. G. (eds.). Advances in Inorganic Biochemistry, Englewood Cliffs: Prentice Hall, 1994, Vol. 9, Chts. 1 and 2.Google Scholar
  42. 42.
    Baker, B. F., “Decapitation” of a 5′-capped oligoribonucleotide by O-phenanthroline: Cu(II), J. Am. Chem. Soc., 1993, 115(8): 3378.CrossRefGoogle Scholar
  43. 43.
    Stern, M. K., Bashkin, J. K., Sall, E. D., Hydrolysis of RNA by transition-metal complexes, J. Am. Chem. Soc., 1990, 112(13): 5357.CrossRefGoogle Scholar
  44. 44.
    Breslow, R., Huang, D-L., Effects of metal ions, including Mg2+ and lanthanides, on the cleavage of ribonucleotides and RNA model compounds. Proc. Natl. Acad. Sci. USA, 1991, 88(10): 4080.CrossRefGoogle Scholar
  45. 45.
    Komiyama, M., Matsumura. K., Matsumoto, Y., Unprecedentedly fast hydrolysis of the RNA dinucleoside monophosphates ApA and UpU by rare earth metal ions, J. Chem. Soc. Chem. Commun., 1992(8): 640.Google Scholar
  46. 46.
    Wrzesinski, J., Michalowski, D., Ciesiolka, J. et al., Specific RNA cleavages induced by manganese ions, FEBS Letters, 1995, 374(1): 62.CrossRefGoogle Scholar
  47. 47.
    Matsumura, K., Komiyama, M., Enormously fast RNA hydrolysis by lanthanide(III) ions under physiological conditions: eminent candidates tor novel tools of biotechnology, J. Biochem., 1997, 122(2): 387.Google Scholar
  48. 48.
    Hayashi, N., Takedu, N., Shiiba, T. et al., Site-selective hydrolysis of RNA by lanthanide metal complexes, Inorg. Chem., 1993. 32(26): 5899.CrossRefGoogle Scholar
  49. 49.
    Morrow, J., Buttrey, L. A., Efficient catalytic cleavage of RNA by lanthanide(III) macrocyclic complexes: toward synthetic nucleates forin vivo applications, J. Am. Chem. Soc., 1992, 114(5): 1903.CrossRefGoogle Scholar
  50. 50.
    Kolasa, K. A., Morrow, J. R., Sharma, A. P., Trivalent lanthanide ions do not cleave RNA in DNA-RNA hybrid, Inorg. Chem., 1993, 32(19): 3983.CrossRefGoogle Scholar
  51. 51.
    Takasaki, B. K., Chin, J., Cleavage of the phosphate diester backbone of DNA with cerium(III) and molecular oxygen, J. Am. Chem. Soc, 1994, 116(3): 1121.CrossRefGoogle Scholar
  52. 52.
    Miyama, S., Asanuma, H., Komiyama, M., Hydrolysis of phosphomonoesters in nucleotides by cerium(IV) ions: Highly selective hydrolysis of monoesters over diester in concentrated buffers, J. Chem. Soc. Perkin Trans. 2, 1997(9): 1685.Google Scholar
  53. 53.
    Kajimura, A., Sumaoka, J., Komiyama, M., DNA hydrolysis by cerium(IV)-saccharide complexes, Carbohydrate Research, 1998, 309(4): 345.CrossRefGoogle Scholar
  54. 54.
    Irisawa, M., Komiyama, M., Hydrolysis of DNA and RNA through cooperation of two metal ions: a novel mimic of phosphoesterases. J. Biochem., 1995, 117(3): 465.Google Scholar
  55. 55.
    Hurst, P., Takasaki, B. K., Chin, J., Rapid cleavage of RNA with a La(III) dimer, J. Am. Chem. Soc., 1996, 118(41): 9982.CrossRefGoogle Scholar
  56. 56.
    Molenveld, P., Kapsabelis, S., Engbersen, J. F. J. et al., Highly efficient phosphate diester transesterification by a calix[4]arene-based dinuclear zinc(II) catalyst, J. Am. Chem. Soc., 1997, 119(12): 2948.CrossRefGoogle Scholar
  57. 57.
    Schnaith, L. M. T., Hanson, R. S., Que, L., Double-stranded cleavage of pBR322 by a diiron complex via a “hydrolytic” mechanism, Proc. Nail. Acad. Sci. USA, 1994. 91(2): 569.CrossRefGoogle Scholar
  58. 58.
    Liu, S., Hamilton, A.D., Rapid and highly base selective RNA cleavage by a dinuclear Cu(II) complex, Chem. Commun., 1999(7): 587.Google Scholar
  59. 59.
    Seo, J. S., Hynes, R. C. Williams, D. et al., Structure and reactivity of dinuclear cobalt(III) complex with peroxide and phosphate diester analogues binding the metal ions, J. Am. Chem. Soc., 1998, 120(38): 9943.CrossRefGoogle Scholar
  60. 60.
    Takeda, N., Imai, T., Irisawa. M. et al., Unprecedentedly fast DNA hydrolysis by the synergism of the cerium(IV)-preseodyniium(III) and the cerium(IV)-neodymium(III) combinations, Chemistry Letters, 1996(8): 599.Google Scholar
  61. 61.
    Irisawa, M., Takeda, N., Komiyama. M., Synergetic catalysis by two non-Ianthanide metal ions for hydrolysis of diribonucleotides. J. Chem. Soc. Chem. Commun., 1995(12): 1221.Google Scholar
  62. 62.
    Komiyama, M., Yoshinari, K., Kinetic analysis of diamine-catalyzed RNA hydrolysis, J. Org. Chem., 1997, 62(7): 2155.CrossRefGoogle Scholar
  63. 63.
    Yoshinari, K., Yamazaki, K., Komiyama, M., Oligoamines as simple and efficient catalysts for RNA hydrolysis, J. Am. Chem. Soc, 1991. 113(15): 5899.CrossRefGoogle Scholar
  64. 64.
    Oivanen, M., Kuusela, S., Lonnberg, H., Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by bronsted acids and bases, Chem. Rev., 1998, 98(3): 961.CrossRefGoogle Scholar
  65. 65.
    Barbier, B., Brack, A., Conformation-controlled hydrolysis of polyribonucleotides by sequential basic polypeptides, J. Am. Chem. Soc., 1992, 114(9): 3511.CrossRefGoogle Scholar
  66. 66.
    Li, X. H., Wan, R., Zhang, Q. et al., The interactions of amino acids and peptides with DNA, in Proceedings of XIV International Conference on Phosphorus Chemistry. Cincinnati, Ohio: Cincinnati Section, American Chemical Society, 1998: 130.Google Scholar
  67. 67.
    Zhao, Y. F., Li, X. H., Ma. Y. et al., Seryl-histidine. phosphoserine, and phosphothreonine used as nucleic acids cleavage agents, Chinese Patent, ZL 96 I 14313.4, 1996.Google Scholar
  68. 68.
    Behmoaras, T., Toulme, J.J., Helene, C., Tryptophan-containing peptide recognized and cleaves DNA at apurinic sites, Nature, 1981, 292(5826): 858.CrossRefGoogle Scholar
  69. 69.
    Pierre, J., Laval, J., Release of 7-methylguanine residues from alkylated DNA by extracts of micrococeus luteus andEscherichia coli. J. Biol. Chem., 1981, 256: 10217.Google Scholar
  70. 70.
    Endo, M., Azuma, Y., Saga, Y. et al., Molecular design for a pinpoint RNA scission, interposition of oligoamines between two DNA oligomers. J. Org. Chem., 1997, 62(4): 846.CrossRefGoogle Scholar
  71. 71.
    Komiyama, M., Inokawa, T., Yoshinari, K., Ethylenediamine-oligo DNA hybrid as sequence-selective artificial ribonuclease, J. Chem. Soc. Chem. Commun., 1995(1): 77.Google Scholar
  72. 72.
    Silnikov, V., Zuber, G., Behr, J. P. et al., Design of ribonuclease mimics for sequence specific cleavage of RNA, Phosphorus Sulfur and Silicon, 1996, 110(1–4): 277.Google Scholar
  73. 73.
    Chen, C-H. B., Gorin, M. B., Sigman, D. S., Sequence specific scission of DNA by the chemical nuclease activity of 1,10-phenanthroline-copper(I) targeted by RNA, Proc. Natl. Acad. Sci. USA, 1993, 90(9): 4206.CrossRefGoogle Scholar
  74. 74.
    Ebrighl, R. H., Ebright, Y. W., Pendergrast, P. S. et al., Conversion of a helix-turn-helix motif sequence-specific DNA binding protein into a site-specific DNA cleavage agent, Proc. Natl. Acad. Sci. USA, 1990, 87(8): 2882.CrossRefGoogle Scholar
  75. 75.
    Nagaoka, M., Hagihara, M., Kuwahara, J. et al., A novel zinc finger-based DNA cutter biosynthetic design and highly selective DNA cleavage. J. Am. Chem. Soc. 1994, 116(9): 4085.CrossRefGoogle Scholar
  76. 76.
    Mack, D. P., Dervan, P. B., Sequence-specific oxidation cleavage of DNA by a designed metalloprotein, Ni(II) · GGH(Hin 139–190), Biochemistry, 1992, 31(39): 9399.CrossRefGoogle Scholar
  77. 77.
    Nielsen, P. E., Egholm, M., Buchardt, O., Peptide nucleic-acid (PNA) — A DNA mimic with a peptide backbone, Bioconjugate Chemistry, 1994. 5(1): 3.CrossRefGoogle Scholar
  78. 78.
    Lohse, J., Hui, C., Sonnichsen, S. H. et al., Sequence selective DNA cleavage by PNA-NTA conjugates, in DNA and RNA Cleavers and Chemotherapy of Cancer and Viral Diseases (ed. Meunier, B.), Dordrecht/Boston/London: Kluwer Academic Publishers, 1995, 133.Google Scholar
  79. 79.
    Footer, M., Egholm, M., Kron, S. et al., Biochemical-evidence that a D-loop is part of a 4-stranded PNA-DNA bundle—nickel-mediated cleavage of duplex DNA by a Gly-Gly-His bis-PNA, Biochemistry, 1996, 35(33): 10673.CrossRefGoogle Scholar
  80. 80.
    Bigey, P., Sonnichsen, S. H., Meunier, B. et al., DNA-binding and cleavage by a cationic manganese porphyrin-peptide nucleic-acid conjugate, Bioconjugate Chemistry, 1997. 8(3): 267.CrossRefGoogle Scholar
  81. 81.
    White, S., Szewczyk, J. W., Turner, J. M. et al., Recognition of the four watson-crick base pairs in the DNA minor groove by synthetic ligands. Nature, 1998, 391(6666): 468.CrossRefGoogle Scholar
  82. 82.
    Wittung, P., Kajanus, J., Edwards, K. et al., Phospholipid membrane-permeability of peptide nucleic-acid, FEBS Letters, 1995, 375(3): 317.CrossRefGoogle Scholar

Copyright information

© Science in China Press 2000

Authors and Affiliations

  1. 1.State Key Laboratory of Bioorganic Phosphorus Chemistry of Education Ministry of China, Department of Chemistry, School of Life Science and EngineeringTsinghua UniversityBeijingChina

Personalised recommendations