Covalently attached oligodeoxyribonucleotides induce RNase activity of a short peptide and modulate its base specifity

Nucleic Acids Research

Volumn 32, Issue 6, 2004, Pages 1928-1936

  Mironova, Nadezhada L ^b   Pyshnyi, Dmtryi V ^b   Ivanova, Eugenya M ^b   Zenkova, Marina A ^b   Gross, Hans J ^a   Vlassov, Valentin V ^b  

^a Institute of Biochemistry   (Germany)

^b INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; ARGININE; GLYCINE; GUANINE; LEUCINE; OLIGODEOXYRIBONUCLEOTIDE; PEPTIDE; PYRIMIDINE; RIBONUCLEASE; RNA;

ARTICLE; CATALYST; CHEMICAL REACTION; COVALENT BOND; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME MECHANISM; ENZYME SUBSTRATE; ENZYME SYNTHESIS; MOLECULAR INTERACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; RNA CLEAVAGE;

AMINO ACID SEQUENCE; ARGININE; BASE SEQUENCE; ENZYME ACTIVATION; HIV-1; KINETICS; LEUCINE; MOLECULAR SEQUENCE DATA; OLIGODEOXYRIBONUCLEOTIDES; OLIGOPEPTIDES; RIBONUCLEASES; RNA; RNA, VIRAL; SUBSTRATE SPECIFICITY;

EID: 3042714203     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh514     Document Type: Article

References (36)

1. Trawick,B.N., Daniher,A.T. and Bashkin,J.K. (1998) Inorganic mimics of ribonucleases and ribozymes: from random cleavage to sequence-specific chemistry to catalytic antisense drugs. Chem. Rev., 98, 939-960.
2. Cowan,J.A. (2001) Chemical nucleases. Curr. Opin. Chem. Biol., 5, 634-642.
3. Bashkin,J.K, Frolova,E.I. and Sampath,U.S. (1994) Sequence-specific cleavage of HIV mRNA by a ribozyme mimic. J. Am. Chem. Soc., 116, 5981-5982.
4. Ushijima,K. and Takaku,H. (1998) Site-specific cleavage of tRNA by imidazole and/or primary amine groups bound at the 5′-end of oligodeoxyribonucleotides. Biochim. Biophys. Acta, 1379, 217-223.
5. Hovinen,J., Guzaev,A., Azhayev,A. and Lonnberg,H. (1995) Imidazole tethered oligodeoxyribonucletides: synthesis and RNA cleaving activity. J. Org. Chem., 60, 2205-2209.
6. Reynolds,M.A., Beck,T.A. and Arnold,L.J. (1996) Antisense oligonucleotide containing an internal, non-nucleotide-based linker promote site-specific cleavage of RNA. Nucleic Acids Res., 24, 760-765.
7. Silnikov,V., Zuber,G., Behi-J.-P., Giege,R. and Vlassov,V. (1996) Design of ribonuclease mimics for sequence specific cleavage of RNA. Phosphorus Sulfur Silicon, 109-110, 277-280.
8. Zhdan,N.S., Kuznetsova,I.L., Vlasov,A.V., Sil'nikov,V.N., Zenkova,M.A. and Vlasov,V.V. (1999) Synthetic ribonucleases. 1. Synthesis and properties of conjugates, containing an RNA-binding fragment based on lysine residues and an RNA hydrolyzing fragment, bearing an imidazole residue. Bioorgan. Khim., 25, 723-732.
9. Lei,G., Arany,I., Tyring,S.K., Brysk,H. and Brysk,M.M. (1998) Zinc-alpha 2-glycoprotein has ribonuclease activity. Arch. Biochem. Biophys., 355, 160-164.
10. Lima,W.F. and Crooke,S.T. (1999) Highly efficient endonucleolytic cleavage of RNA by a Cys(2)His(2) zinc-finger peptide. Proc. Natl Acad. Sci. USA, 96, 10010-10015.
11. Barbier,B. and Brack,A. (1987) Search for catalytic properties of simple polypeptides. Orig. Life Evol. Biosph., 17, 381-390.
12. Barbier,B. and Brack,A. (1988) Basic polypeptides accelerate the hydrolysis of ribonucleic acids. J. Am. Chem. Soc., 110, 6880-6882.
13. Brack,A. and Barbier,B. (1990) Chemical activity of simple basic peptides. Orig. Life Evol. Biosph., 20, 139-144.
14. Pyshnyi,D.V., Repkova,M.N., Lokhov,S.G., Ivanova,E.M., Venyaminova,A.G. and Zarytova,V.F. (1997) Artificial ribonucleases. 1. Site-directed RNA cleavage by 5′-peptidyloligodeoxyribonucleotides containing arginine and leucine residues. Bioorg. Khim., 23, 497-504.
15. Pyshnyi,D., Repkova,M., Lokhov,S., Ivanova,E., Venyaminova,A. and Zarytova,V. (1997) Oligonucleotide-peptide conjugates for RNA cleavage. Nucl. Nucl. Nucleic Acids, 16, 1571-1574.
16. Mironova,N.L., Pyshnyi,D.V., Ivanova,E.M., Zarytova,V.F., Zenkova,M.A., Gross,H.J. and Vlassov,V.V. (2002) Sequence-specific cleavage of the target RNA with oligonucleotide-peptide conjugates. Russ. Chem. Bull., 51, 1177-1186.
17. Dock-Bregeon,A.C. and Moras,D. (1987) Conformational changes and dynamics of tRNAs: evidence from hydrolysis patterns. Cold Spring Harb. Symp. Quant. Biol., 52, 113-121.
18. Morrow,J.R. (1994) Artificial ribonucleases. Adv. Inorg. Biochem., 9, 41-74.
19. Kierzek,R. (1992) Hydrolysis of oligoribonucleotides: influence of sequence and length. Nucleic Acids Res., 20, 5079-5084.
20. Bibillo,A., Figlerowicz,M. and Kierzek,R. (1999) The non-enzymatic hydrolysis of oligoribonucleotides VI. The role of biogenic polyamines. Nucleic Acids Res., 27, 3931-3937.
21. Zarytova,V.F., Ivanova,E.M., Yarmoluk,S.N. and Alekseeva,I.V. (1988) Synthesis of oligonucleotidyl-(5′-N)-peptides containing arginine. Biopolym. Cell, 1, 220-222.
22. Milligan,J.F. and Unlenbeck,O.C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol., 180, 51-62.
23. 32P-labeling in the sequence analysis of nonradioactive tRNAs. Methods Enzymol., 59, 58-109.
24. England,T.E., Bruce,A.G. and Uhlenbeck,O.C. (1980) Specific labelling of 3′ termini of RNA with T4 RNA ligase. Methods Enzymol., 65, 65-74.
25. Vlasov,A.V., Vlasov,V.V. and Giege,R. (1996) RNA hydrolysis catalyzed by imidazole as a reaction for studying the secondary structure of RNA and complexes of RNA with oligonucleotides. Dokl. Akad. Nauk, 349, 411-413.
26. Donis-Keller,H., Maxam,A.M. and Gilbert,W. (1977) Mapping adenines, guanines and pyrimidines in RNA. Nucleic Acids Res., 4, 2527-2538.
27. Benson,S.W. (1960) Mathematical characterization of complex kinetic systems. In Fernelius,W.C., Hammett,L.P., Hume,D.N., Pople,J.A., Roberts,J.D. and Williams,H.H. (eds.), The Foundations of Chemical Kinetics. McGraw-Hill, New York, pp. 33-49.
28. Varfolomeev,S.D. and Gurevich,K.G. (1999) Enzymatic catalysis. In Ostrovskii,M.A. and Sergeev,G.B. (eds), Biokinetics - Practical Course. FAIR Press, Moscow, p. 92.
29. Isel,C., Ehresmann,C., Keith,G., Ehresmann,B. and Marquet,R. (1995) Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer). J. Mol. Biol., 247, 236-250.
30. Mironova,N.L., Pyshnyi,D.V., Ivanova,E.M., Zenkova,M.A., Gross,G.J. and Vlasov,V.V. (2002) Artificial ribonucleases: oligonucleotide-peptide conjugates that cleave RNA at the GpX and PypA phosphodiester bonds. Dokl. Biochem. Biophys., 385, 196-200.
31. Höschler,K., Hoier,H., Hubner,B., Saenger,W., Orth,P. and Hahn,U. (1999) Structural analysis of an RNase T1 variant with an altered guanine binding segment. J. Mol. Biol., 294, 1231-1238.
32. Emanuel',N.M. and Knorre,D.G. (1973) Chemical Kinetics. Homogeneous Reactions. Hulsted Press-John Wiley, New York.
33. Puglishi,J.D., Tan,R., Calnan,B.J., Frankel,A.D. and Williamson,J.R. (1992) Conformation of the TAR RNA-arginine complex NMR spectroscopy. Science, 257, 76-80.
34. Pace,C.N., Heinemann,U., Hahn,U. and Saenger,W. (1991) Ribonuclease T1: structure, function and stability. Angew. Chem., 30, 343-360.
35. Sermon,B.A., Lowe,P.N., Strom,M. and Eccleston,J.F. (1998) The importance of two conserved arginine residues for catalysis by the Ras GTPase-activating protein, neurofibromin. J. Biol. Chem., 273, 9480-9485.
36. Luscombe,N.M., Laskowski,R.A. and Thornton,J.M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.