ESPSearch: A program for finding exact sequences and patterns in DNA, RNA, or protein

BioTechniques

Volumn 38, Issue 1, 2005, Pages 109-115

  Watt, Terry J ^a   Doyle, Donald F ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DATABASE SYSTEMS; GENES; NUCLEIC ACIDS; PATTERN RECOGNITION; PROTEINS; RNA; WEBSITES;

HOMODIMERIC PROTEINS; HUMAN PROTEOME; LARGE SCALES; PROTEIN LIBRARIES;

COMPUTER PROGRAM LISTINGS;

DIMER; PROTEIN BAX; PROTEIN P53; PROTEOME; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR; ZINC FINGER PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; COMPUTER PROGRAM; DATA BASE; DNA SEQUENCE; EQUIPMENT DESIGN; GENOME; PROMOTER REGION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; RNA SEQUENCE;

EID: 12344286861     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/05381RR03     Document Type: Article

References (22)

1. Matys, V., E. Fricke, R. Geffers, E. Gößling, M. Haubrock, R. Hehl, K. Hornischer, D. Karas, et al. 2003. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31:374-378.
2. Altschul, S.F., W. Gish, W. Miller, E.W. Meyers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 275:403-410.
3. Falquet, L., M. Pagni, P. Bucher, N. Hulo, C.J.A. Sigrist, K. Hofmann, and A. Bairoch. 2002. The PROSITE database, its status in 2002. Nucleic Acids Res. 30:235-238.
4. Rice, P., I. Longden, and A. Bleasby. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16:276-277.
5. Grillo, G., F. Licciulli, S. Liuni, E. Sbisa, and G. Pesole. 2003. PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res. 31:3608-3612.
6. Vousden, K.H. and X. Lu. 2002. Live or let die: the cell's response to p53. Nat. Rev. Cancer 2:594-604.
7. Beerli, R.R. and C.F. Barbas, 3rd. 2002. Engineering polydactyl zinc-finger transcription factors. Nat. Biotechnol. 20:135-141.
8. Jantz, D., B.T. Amann, G.J. Gatto, Jr., and J.M. Berg. 2004. The design of functional DNA-binding proteins based on zinc finger domains. Chem. Rev. 104:789-800.
9. Falke, D., M. Fisher, D. Ye, and R.L. Juliano. 2003. Design of artificial transcription factors to selectively regulate the pro-apoptotic bax gene. Nucleic Acids Res. 57:e10.
10. Bae, K.H., Y. Do Kwon, H.C. Shin, M.S. Hwang, E.H. Ryu, K.S. Park, H.Y. Yang, D.K. Lee, et al. 2003. Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat. Biotechnol. 21:275-280.
11. Ptashne, M. 1992. A Genetic Switch. Blackwell Scientific Publications and Cell Press, Cambridge, MA.
12. Kohler, J.J., S.J. Metallo, T.L. Schneider, and A. Schepartz. 1999. DNA specificity enhanced by sequential binding of protein monomers. Proc. Natl. Acad. Sci. USA 96:11735-11739.
13. Kohler, J.J. and A. Schepartz. 2001. Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors. Bioorg. Med. Chem. 9:2435-2443.
14. Wolfe, S.A., R.A. Grant, and C.O. Pabo. 2003. Structure of a designed dimeric zinc finger protein bound to DNA. Biochemistry 42:13401-13409.
15. Fortin, A., S.P. Cregan, J.G. MacLaurin, N. Kushwaha, E.S. Hickman, C.S. Thompson, A. Hakim, P.R. Albert, et al. 2001. APAF1 is a key transcriptional target for p53 in the regulation of neuronal cell death. J. Cell Biol. 155:207-216.
16. Miyashita, T. and J.C. Reed. 1995. Tumor suppressor p53 is a direct transcriptional activator of the human bax gene. Cell 80:293-299.
17. Bourdon, J.C., V. Deguin-Chambon, J.C. Lelong, P. Dessen, P. May, B. Debuire, and E. May. 1997. Further characterisation of the p53 responsive element - identification of new candidate genes for trans-activation by p53. Oncogene 14:85-94.
18. Oda, K., H. Arakawa, T. Tanaka, K. Matsuda, C. Tanikawa, T. Mori, H. Nishimori, K. Tamai, et al. 2000. p53AIP1, a potential mediator of p53-dependent apoptosis, and its regulation by Ser-46-phosphorylated p53. Cell 102:849-862.
19. Stambolic, V., D. MacPherson, D. Sas, Y. Lin, B. Snow, Y. Jang, S. Benchimol, and T.W. Mak. 2001. Regulation of PTEN transcription by p53. Mol. Cell 8:317-325.
20. Snøve, O., Jr. and T. Holen. 2004. Many commonly used siRNAs risk off-target activity. Biochem. Biophys. Res. Commun. 319:256-263.
21. Heery, D.M., E. Kalkhoven, S. Hoare, and M.G. Parker. 1997. A signature motif in transcriptional co-activators mediates binding to nuclear receptors. Nature 337:733-736.
22. Chang, C., J.D. Norris, H. Grøn, L.A. Paige, P.T. Hamilton, D.J. Kenan, D. Fowlkes, and D.P. McDonnell. 1999. Dissection of the LXXLL nuclear receptor-coactivator interaction motif using combinatorial peptide libraries: discovery of peptide antagonists of estrogen receptors alpha and beta. Mol. Cell. Biol. 19:8226-8239.