The simple and rapid detection of specific PCR products from bacterial genomes using Zn finger proteins

Nucleic Acids Research

Volumn 36, Issue 11, 2008, Pages

  Osawa, Yuko ^a   Ikebukuro, Kazunori ^a   Motoki, Hiroaki ^b   Matsuo, Takafumi ^b   Horiuchi, Michio ^b   Sode, Koji ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^b SYSTEM INSTRUMENTS Co Ltd   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; FLHA PROTEIN; TRANSCRIPTION FACTOR SP1; ZINC FINGER PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BACTERIAL GENOME; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; FLUORESCENCE ANALYSIS; GEL ELECTROPHORESIS; GENE AMPLIFICATION; LEGIONELLA PNEUMOPHILA; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; BACTERIUM; BINDING SITE; CHEMISTRY; DNA SEQUENCE; EVALUATION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); LEGIONELLA PNEUMOPHILA;

BACTERIA; BINDING SITES; DNA-BINDING PROTEINS; ENZYME-LINKED IMMUNOSORBENT ASSAY; GENOME, BACTERIAL; HUMANS; LEGIONELLA PNEUMOPHILA; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SP1 TRANSCRIPTION FACTOR; ZINC FINGERS;

EID: 46349092766     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn274     Document Type: Article

References (39)

1. Lazcka,O., Del Campo,F.J. and Munoz,F.X. (2007) Pathogen detection: A perspective of traditional methods and biosensors. Biosens. Bioelectron., 22, 1205-1217.
2. Monis,P.T. and Gigho,S. (2006) Nucleic acid amplification-based techniques for pathogen detection and identification. Infect. Genet. Evol., 6, 2-12.
3. Johnson-White,B., Lin,B. and Ligler,F.S. (2007) Combination of immunosensor detection with viability testing and confirmation using the polymerase chain reaction and culture. Anal. Chem., 79, 140-146.
4. Call,D.R., Borucki,M.K. and Loge,F.J. (2003) Detection of bacterial pathogens in environmental samples using DNA micro-arrays. J. Microbiol. Methods, 53, 235-243.
5. Tawa,K., Yao,D. and Knoll,W. (2005) Matching base-pair number dependence of the kinetics of DNA-DNA hybridization studied by surface plasmon fluorescence spectroscopy. Biosens. Bioelectron., 21, 322-329.
6. Tsuruoka,M., Yano,K., Ikebukuro,K., Nakayama,H., Masuda,Y. and Yarube,I. (1996) Optimization of the rate of DNA hybridization and rapid detection of methicillin resistant Staphylococcus aureus DNA using fluorescence polarization. J. Biotechnol., 48, 201-208.
7. Kai,E., Ikebukuro,K., Hoshina,S., Watanabe,H. and Karube.I. (2000) Detection of PCR products of Escherichia coli O157:H7 in human stool samples using surface plasmon resonance (SPR). FEMS Immunol. Med. Microbiol., 29, 283-288.
8. Miyachi,H., Ikebukuro,K., Yano,K., Aburatani,H. and Karube,I. (2004) Single nucleotide polymorphism typing on DNA array with hydrophobic surface fabricated by plasma-polymerization technique. Biosens. Bioelectrn., 20, 184-189.
9. Klug,A. and Schwabe,J.W. (1995) Protein motifs 5. Zinc fingers. FASEB J., 9, 597-604.
10. Mackay,J.P. and Crossley,M. (1998) Zinc fingers are sticking together. Trends Biochem. Sci., 23, 1-4.
11. Sanchez-Garcia,I. and Rabbitts,T.H. (1994) The LIM domain: A new structural motif found in zinc-finger-like proteins. Trends Genet. 10, 315-320.
12. Iuchi,S. (2001) Three classes of C2H2 zinc finger proteins. Cell. Mol. Life Sci., 58, 625-635.
13. Wolfe,S.A., Nekludova,L. and Pabo,C.O. (2000) DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183-212.
14. Greisman,H.A. and Pabo,C.O. (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science, 275, 657-661.
15. Isalan,M., Klug,A. and Choo,Y. (2001) A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nat. Biotechnol., 19, 656-660.
16. Dreier,B., Beerli,R.R., Segal,D.J., Flippin,J.D. and Barbas,C.F.,III (2001) Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors. J. Biol. Chem., 276, 29466-29478.
17. Sera,T. and Uranga,C. (2002) Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. Biochemistry 41, 7074-7081.
18. Mandell,J.G. and Barbas,C.F.,III (2006) Zinc finger tools: Custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res., 34, W516-W523.
19. Dhanasekaran,M., Negi,S. and Sugiura,Y. (2006) Designer zinc finger proteins: Tools for creating artificial DNA-binding functional proteins. Acc. Chem. Res., 39, 45-52.
20. Papworth,M., Kolasinska,P. and Minczuk,M. (2006) Designer zinc-finger proteins and their applications. Gene, 366, 27-38.
21. Urnov,F.D., Miller,J.C., Lee,Y.L., Beausejour,C.M., Rock,J.M., Augustus,S., Jamieson,A.C., Porteus,M.H., Gregory,P.D. and Holmes,M.C. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature, 435, 646-651.
22. Beerli,R.R., Dreier,B. and Barbas,C.F.,III (2000) Positive and negative regulation of endogenous genes by designed transcription factors. Proc. Natl Acad. Sci. USA, 97, 1495-1500.
23. Varshavsky,A. (20H7) From the cover: Targeting the absence: homozygous DNA deletions as immutable signposts for cancer therapy. Proc. Natl Acad. Sci, USA, 104, 14935-14940.
24. Ooi,A.T., Stains,C.I., Ghosh,I. and Segal,D.J. (2006) Sequence-enabled reassembly of beta-lactamase (SEER-LAC): A sensitive method for the detection of double-stranded DNA. Biochemistry, 45, 3620-3625.
25. Stains,C.I., Porter,J.R., Ooi,A.T., Segal,D.J. and Ghosh,I. (2005) DNA sequence-enabled reassembly of the green fluorescent protein. J. Am. Chem. Soc., 127, 10782-10783.
26. Stains,C.I., Furman,J.L., Segal,D.J. and Ghosh,I. (2006) Site-specific detection of DNA methylation utilizing mCpG-SEER. J. Am. Chem. Soc. 128, 9761-9765.
27. Takeuchi,A. and Sode,K. (2000) A Salmonella detection system using an engineered DNA binding protein that specifically captured a DNA sequence. Anal. Chem., 72, 2809-2813.
28. Pavletich,N.P. and Pabo,C.O. (1991) Zinc finger-DNA recognition: Crystal structure of a Zi1268-DNA complex at 2.1 A. Science, 252, 809-817.
29. Yokono,M., Saegusa,N., Matsushita,K. and Sugiura,Y. (1994) Unique DNA binding mode of the N-terminal zinc finger of transcription factor Sp1. Biochemistry, 37, 6824-6832.
30. Oka,S., Shiraishi,V., Yoshida,T., Ohkubo,T., Sugiura,Y. and Kobayashi,Y. (2004) NMR structure of transcription factor Sp1 DNA binding domain. Biochemistry, 43, 16027-16035.
31. Amemura-Maekawa,J., Kura,F., Chang,B. and Watanabe,H. (2005) Legionella pneumophila serogroup 1 isolates from cooling towers in Japan for in a distinct genetic cluster. Microbiol. Immunol., 49, 1027-1033.
32. Fujimura,S., Oka,T., Tooi,O., Meguro,M., Chiba,M., Kawamura,M., Maki,F., Takeda,H. and Watanabe,A. (2006) Detection of Legionella pneumophila serogroup 7 strain from bathwater samples in a Japanese hospital. J. Infect. Chemother., 12, 105-108.
33. Lee,T.C., Vickers,R.M., Yu,V.L. and Wagener,M.M. (1993) Growth of 28 Legionella species on selective culture media: A comparative study. J. Clin. Microbiol., 31, 2764-2768.
34. Leskela,T., Tilsala-Timisjarvi,A., Kusnetsov,J., Neubauer,P. and Breitenstein,A. (2005) Sensitive genus-specific detection of Legionella by a 16S rRNA based sandwich hybridization assay. J. Microbiol. Methods, 62, 167-179.
35. Stolhaug,A. and Bergh,K, (2006) Identification and differentiation of Legionella pneumophila and Legionella spp. with real-time PCR targeting the 16S rRNA gene and species identification by mip sequencing. Appl. Environ. Microbiol., 72, 6394-6398.
36. Wilson,D A., Yen-Lieberman,B., Reischl,U., Gordon,S.M. and Procop,G.W. (2003) Detection of Legionella pneumophila by real-time PCR for the mip gene. J. Clin. Microbiol., 41, 3327-3330.
37. Fiume,L., Bucci Sabattini,M.A. and Poda,G. (2005) Detection of Legionelia pneumophila in water samples by species-specific real-time and nested PCR assays. Lett. Appl. Microbiol., 41, 470-475.
38. Green,A. and Sarkar,B, (1998) Alteration of zif68 zinc-finger motifs gives rise to non-native zinc-co-ordination sites but preserves wild-type DNA recognition. Biochem. J., 333, 85-90.
39. Chien,M., Morozova,I., Shi,S., Sheng,H., Chen,J., Gomez,S.M., Asamani,G., Hill,K., Nuara,J., Feder,M. et al. (2004) The genomic sequence of the accidental pathogen Legionella pneumophila. Science 305, 1966-1968.