Interaction of C5 protein with RNA aptamers selected by SELEX

Nucleic Acids Research

Volumn 30, Issue 24, 2002, Pages 5360-5368

  Lee, June Hyung ^a   Kim, Hana ^a   Ko, Jaehyeong ^a   Lee, Younghoon ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; APTAMER; ESCHERICHIA COLI PROTEIN; MAGNESIUM ION; PROTEIN C5; RIBONUCLEASE P; RNA; UNCLASSIFIED DRUG;

ANALYTIC METHOD; BINDING AFFINITY; COMPLEX FORMATION; CONCENTRATION RESPONSE; CONTROLLED STUDY; DISSOCIATION CONSTANT; ESCHERICHIA COLI; HYDROPHOBICITY; MOLECULAR STABILITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; REVIEW; RNA ANALYSIS; SEQUENCE ANALYSIS;

BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; BINDING, COMPETITIVE; ESCHERICHIA COLI PROTEINS; GENETIC TECHNIQUES; KINETICS; LIGANDS; MAGNESIUM; MUTATION; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; OSMOLAR CONCENTRATION; QUATERNARY AMMONIUM COMPOUNDS; RIBONUCLEASE P; RNA-BINDING PROTEINS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0037115895     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf694     Document Type: Review

References (34)

1. Kurz,J.C. and Fierke,C.A. (2000) Ribonuclease P: a ribonucleoprotein enzyme. Curr. Opin. Chem. Biol., 4, 553-558.
2. Frank,D.N. and Pace,N.R. (1998) Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem., 67, 153-180.
3. Park,B.H., Choi,Y.N., Park,J.W., Sim,S., Gil,M.C., Kim,S., Kim,M. and Lee,Y. (1998) Expression of C5 protein, the protein component of Escherichia coli RNase P, from the tac promoter. Mol. Cells, 8, 96-100.
4. Liu,F. and Altman,S. (1994) Differential evolution of substrates for an RNA enzyme in the presence and absence of its protein cofactor. Cell, 77, 1093-1100.
5. Komine,Y., Kitabatake,M., Yokogawa,T., Nishikawa,K. and Inokuchi,H. (1994) A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc. Natl Acad. Sci. USA, 91, 9223-9227.
6. Liu,F. and Altman,S. (1996) Requirements for cleavage by a modified RNase P of a small model substrate. Nucleic Acids Res., 24, 2690-2696.
7. Guerrier-Takada,C., van Belkum,A., Pleij,C.W. and Altman,S. (1988) Novel reactions of RNAase P with a tRNA-like structure in turnip yellow mosaic virus RNA. Cell, 53, 267-272. '
8. Guerrier-Takada,C., Gardiner,K., Marsh,T., Pace,N. and Altman,S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35, 849-857.
9. Kim,J.J., Kilani,A.F., Zhan,X., Altman,S. and Liu,F. (1997) The protein cofactor allows the sequence of an RNase P ribozyme to diversify by maintaining the catalytically active structure of the enzyme. RNA, 3, 613-623.
10. Niranjanakumari,S., Stams,T., Crary,S.M., Christianson,D.W. and Fierke,C.A. (1998) Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA. Proc. Natl Acad. Sci. USA, 95, 15212-15217.
11. Lumelsky,N. and Altman,S. (1988) Selection and characterization of randomly produced mutants in the gene coding for M1 RNA. J. Mol. Biol., 202, 443-454.
12. Phe bearing a single mismatch in the acceptor stem. Biochem. Biophys. Res. Commun., 268, 136-140.
13. Stams,T., Niranjanakumari,S., Fierke,C.A. and Christianson,D.W. (1998) Ribonuclease P protein structure: evolutionary origins in the translational apparatus. Science, 280, 752-755.
14. Spitzfaden,C., Nicholson,N., Jones,J.J., Guth,S., Lehr,R., Prescott,C.D., Hegg,L.A. and Eggleston,D.S. (2000) The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA. J. Mol. Biol., 295, 105-115.
15. Vioque,A., Arnez,J. and Altman,S. (1988) Protein-RNA interactions in the RNase P holoenzyme from Escherichia coli. J. Mol. Biol., 202, 835-848.
16. Talbot,S.J. and Altman,S. (1994) Gel retardation analysis of the interaction between C5 protein and M1 RNA in the formation of the ribonuclease P holoenzyme from Escherichia coli. Biochemistry, 33, 1399-1405.
17. Johansson,H.E., Dertinger,D., LeCuyer,K.A., Behlen,L.S., Greef,C.H. and Uhlenbeck,O.C. (1998) A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein. Proc. Natl Acad. Sci. USA, 95, 9244-9249.
18. Zhang,J., Tamilarasu,N., Hwang,S., Garber,M.E., Huq,I., Jones,K.A. and Rana,T.M. (2000) HIV-1 TAR RNA enhances the interaction between Tat and cyclin T1. J. Biol. Chem., 275, 34314-34319.
19. Kole,R., Baer,M.F., Stark,B.C. and Altman,S. (1980) E. coli RNAase P has a required RNA component. Cell, 19, 881-887.
20. Gold,L., Polisky,B., Uhlenbeck,O. and Yarus,M. (1995) Diversity of oligonucleotide functions. Annu. Rev. Biochem., 64, 763-797.
21. Schneider,D., Tuerk,C. and Gold,L. (1992) Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. J. Mol. Biol., 228, 862-869.
22. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory Mannual, 2nd Edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. Kim,M., Park,B.H. and Lee,Y. (2000) Effects of terminal deletions in C5 protein on promoting RNase P catalysis. Biochem. Biophys. Res. Commun., 268, 118-123.
24. Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
25. Talbot,S.J. and Altman,S. (1994) Kinetic and thermodynamic analysis of RNA-protein interactions in the RNase P holoenzyme from Escherichia coli. Biochemistry, 33, 1406-1411.
26. Lindell,M., Romby,P. and Wagner,E.G. (2002) Lead(II) as a probe for investigating RNA structure in vivo. RNA, 8, 534-541.
27. Zarrinkar,P.P., Wang,J. and Williamson,J.R. (1996) Slow folding kinetics of RNase P RNA. RNA, 2, 564-573.
28. Lago,H., Parrott,A.M., Moss,T., Stonehouse,N.J. and Stockley,P.G. (2001) Probing the kinetics of formation of the bacteriophage MS2 translational operator complex: identification of a protein conformer unable to bind RNA. J. Mol. Biol., 305, 1131-1144.
29. Allain,F.H., Howe,P.W., Neuhaus,D. and Varani,G. (1997) Structural basis of the RNA-binding specificity of human U1A protein. EMBO J., 16, 5764-5772.
30. van Gelder,C.W., Gunderson,S.I., Jansen,E.J., Boelens,W.C., Polycarpou-Schwarz,M., Mattaj,I.W. and van Venrooij,W.J. (1993) A complex secondary structure in U1A pre-mRNA that binds two molecules of U1A protein is required for regulation of polyadenylation. EMBO J., 12, 5191-5200.
31. Tsai,D.E., Harper,D.S. and Keene,J.D. (1991) U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts. Nucleic Acids Res., 19, 4931-4936.
32. Oubridge,C., Ito,N., Evans,P.R., Teo,C.H. and Nagai,K. (1994) Crystal structure at 1.92 AÌ resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature, 372, 432-438.
33. Hall,K.B. (1994) Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain. Biochemistry, 33, 10076-10088.
34. Scherly,D., Dathan,N.A., Boelens,W., van Venrooij,W.J. and Mattaj,I.W. (1990) The U2B" RNP motif as a site of protein-protein interaction. EMBO J., 9, 3675-3681.