Identification of a biologically significant DNA-binding peptide motif by use of a random phage display library

Gene

Volumn 171, Issue 1, 1996, Pages 1-8

  Cheng, X ^a   Kay, B K ^b   Juliano, R L ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Combinatorial library; Oligodeoxyribonucleotide; Ribonucleoprotein; Selectivity; Single strand binding protein

Indexed keywords

DNA BINDING PROTEIN; DOUBLE STRANDED DNA; OLIGODEOXYRIBONUCLEOTIDE; PEPTIDE; SINGLE STRANDED DNA;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; DNA SEQUENCE; ESCHERICHIA COLI; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN DNA BINDING;

EID: 0029934724     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/0378-1119(95)00889-6     Document Type: Article

References (38)

1. Brunel, F., Alzari, P.M., Ferrara, P. and Zakin, M.N.: Cloning and sequencing of PYBP, a pyrimidine-rich specific single DNA-binding protein. Nucleic Acids Res. 19 (1991) 5237-5245.
2. Burd, C.G. and Dreyfuss, G.: Conserved structures and diversity of functions of RNA-binding proteins. Science 265 (1994) 615-621.
3. Casas-Finet, J.R., Khamis, M.I., Maki, A.H. and Chase, J.W.: Tryptophan 54 and phenylalanine 60 are involved synergistically in the binding of E. coli SSB protein to single-stranded polynucleotides. FEBS Lett. 220 (1987) 347-352.
4. Cheadle, C., Ivashchenko, Y., South, V., Searfoss, G.H., French, S., Howk, R., Ricca, G.A. and Jaye, M.: Identification of a Src SH3 domain binding motif by screening a random phage display library. J. Biol. Chem. 269 (1994) 24034-24039.
5. Choo, Y. and Klug, A.: A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA. Nucleic Acids Res. 21 (1993) 3341-3346.
6. Choo, Y. and Klug, A.: Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc. Natl. Acad. Sci. USA 91 (1994a) 11168-11172.
7. Choo, Y. and Klug, A.: Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc. Natl. Acad. Sci. USA 91 (1994b) 11163-11167.
8. Choo, Y., Sánchez-Garcia, I. and Klug, A.: In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence. Nature 372 (1994) 642-645.
9. De Vries, J. and Wackernagel, W.: Cloning and sequencing of the Serratia marcescens gene encoding a single-stranded DNA-binding protein (SSB) and its promoter region. Gene 127 (1993) 39-45.
10. De Vries, J. and Wackernagel, W.: Cloning and sequencing of the Proteus mirabilis gene for a single-stranded DNA-binding protein (SSB) and complementation of Escherichia coli ssb point and deletion mutations. Microbiology 140 (1994) 889-895.
11. De Vries, J., Genschel, J., Urbanke, C., Thole, H. and Wackernagel, W.: The single-stranded-DNA-binding proteins (SSB) of Proteus mirabilis and Serratia marcescens. Eur. J. Biochem. 224 (1994) 613-622.
12. Devlin, J.J., Panganiban, L.C. and Devlin, P.E.: Random peptide libraries: a source of specific protein binding molecules. Science 249 (1990) 404-406.
13. Dynan, W.S. and Tjian, R.: The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter. Cell 35 (1983) 79-87.
14. Fowlkes, D.M., Adams, M.D., Fowler, V.A. and Kay, B.K.: Multipurpose vectors for peptide expression on the M13 viral surface. Biotechniques 13 (1992) 422-428.
15. Garner, M.M. and Revzin, A.: A gel electrophoresis method for quantifying the binding of proteins to specific DNA region: application to components of Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 9 (1981) 3047-3060.
16. Geierstanger, B.H., Mrksich, M., Dervan, P.B. and Wemmer, D.E.: Design of a GC-specific DNA minor groove-binding peptide. Science 266 (1994) 646-650.
17. Hunger, H.-D., Coutelle, C., Behrendt, G., Flachmeier, C., Rosenthal, A., Speer, R.A., Breter, H., Szargan, R., Franke, P., Stahl, P.F., Cuong, N.V. and Barchend, G.: CCA paper: a new two-dimensional cyanuric chloride-activated matrix for universal application in molecular biology. Anal. Biochem. 156 (1986) 286-299.
18. Kay, B.K., Adey, N.B., He, Y.S., Manfredi, J.P., Mataragnon, A.H. and Fowlkes, D.M.: An M13 phage library displaying random 38-amino-acid peptides as a source of novel sequences with affinity to selected targets. Gene 128 (1993) 59-65.
19. Kay, B.K.: Biologically displayed random peptides as reagents for mapping protein-protein interactions. Perspect. Drug Discov. Design 2 (1995) in press.
20. Kenan, D.J., Query, C.C. and Keene, J.D.: RNA recognition: towards identifying determinants of specificity. Trends Biochem. Sci. 16 (1991) 214-220.
21. Koivunen, E., Wang, B. and Ruoslahti, E.: Isolation of a highly specific ligand for the α5β1 integrin from a phage display library. J. Cell Biol. 124 (1994) 373-380.
22. Krook, M., Mosbach, K. and Lindbladh, C.: Selection of peptides with affinity for single stranded DNA using a phage display library. Biochem. Biophys. Res. Commun. (1994) 204:849-854
23. Lohman, T.M. and Ferrari, M.E.: Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu. Rev. Biochem. 63 (1994) 527-570.
24. Merrill, B.M., Williams, K.R., Chase, J.W. and Konigsberg, W.H.: Photochemical cross-linking of the Eschericia coli single-stranded DNA-binding protein to oligonucleotides. Identification of phenyl-alanine 60 as the site of cross-linking. J. Biol. Chem. 259 (1984) 10850-10856.
25. Oldenburg, K.R., Loganathan, D., Goldstein, I.J., Schultz, P.G. and Gallop, M.A.: Peptide ligands for a sugar-binding protein isolated from a random peptide library. Proc. Natl. Acad. Sci. U.S.A 89 (1992) 5359-5397.
26. Pabo, C.O. and Sauer, R.T.: Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61 (1992) 1053-1095.
27. Parmley, S.F. and Smith, G.P.: Antibody selectable filamentous fd phage vectors: affinity purification of target genes. Gene 73 (1988) 305-318.
28. Parmley, S.F and Smith G.P.: Filamentous fusion phage cloning vectors for the study of epitopes and design of vaccines. Adv. Exp. Med. Biol. 251 (1989) 215-218
29. Rebar, E.J. and Pabo, C.O.: Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 263 (1994) 671-673.
30. Rickles, R.J., Botfield, M.C., Weng, Z., Taylor, J.A., Green, O.M., Brugge, J.S. and Zoller, M.J.: Identification of Src, Fyn, Lyn, PI3K and Abl SH3 domain ligands using phage display libraries. EMBO J. 13 (1994) 5598-5604.
31. Sambrook, J., Fritsch, E.F. and Maniatis, T.: Molecular Cloning. A Laboratory Manual. CSHL Press, Cold Spring Harbor Laboratory, NY, 1989, pp. 4.3-13.6
32. Sancar, A., Williams, K.R., Chase, J.W. and Rupp, W.D.: Sequences of the ssb gene and protein. Proc. Natl. Acad. Sci. USA 78 (1981) 4274-4278.
33. Scott, J.K. and Smith, G.P.: Searching for peptide ligands with an epitope library. Science 249 (1990) 386-390.
34. Scott, J.K., Loganathan, D., Easley, R.B., Gong, X. and Goldstein, I.J.: A family of concanavalin A-binding peptides from a hexapeptide epitope library. Proc. Natl. Acad. Sci. USA 89 (1992) 5398-5402.
35. Smith, N.L. and Lenhoff, H.M.: Covalent binding of proteins and glucose-6-phosphate dehydrogenase to cellulosic carriers activated with s-triazine trichloride. Anal. Biochem. 61 (1974) 392-415.
36. Sparks, A.B., Quilliam, L.A., Thorn, J.M., Der, C.J. and Kay, B.K.: Identification and characterization of Src SH3 ligands from phage-displayed random peptide libraries. J. Biol. Chem. 269 (1994) 23853-23856.
37. Stroumbakis, N.D., Li, Z. and Tolias, P.P.: RNA-and single-stranded DNA-binding (SSB) proteins expressed during Drosophila melanogaster oogenesis: a homolog of bacterial and eukaryotic mitochondrial SSBs. Gene 143 (1994) 171-177.
38. Van Ness, J., Kalbfleisch, S., Petrie, C.R., Reed, M.W., Tabone, J.C. and Vermeulen, N.M J.: A versatile solid support system for oligodeoxy-nucleotide probe-based hybridization assays. Nucleic Acids Res. 19 (1991) 3345-3350.