Hairpin Primers for Simplified Single-Nucleotide Polymorphism Analysis of Mycobacterium tuberculosis and Other Organisms

Journal of Clinical Microbiology

Volumn 42, Issue 3, 2004, Pages 1236-1242

  Hazbón, Manzour Hernando ^a   Alland, David ^a  

^a RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYE; HAIRPIN PRIMER; ISONIAZID; PRIMER DNA; UNCLASSIFIED DRUG;

ALLELE; AMPLIFICATION REFRACTORY MUTATION SINGLE NUCLEOTIDE POLYMORPHISM; ANTIBIOTIC RESISTANCE; ARTICLE; DIAGNOSTIC ACCURACY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; CHROMOSOMES, BACTERIAL; COMPUTER SYSTEMS; DNA PRIMERS; DNA, BACTERIAL; MYCOBACTERIUM TUBERCULOSIS; NUCLEIC ACID CONFORMATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY;

ACTINOBACTERIA (CLASS); MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; UNCULTURED ACTINOMYCETE;

EID: 1542409116     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.3.1236-1242.2004     Document Type: Article

References (33)

1. Abate, G., S. E. Hoffner, V. O. Thomsen, and H. Miorner. 2001. Characterization of isoniazid-resistant strains of Mycobacterium tuberculosis on the basis of phenotypic properties and mutations in katG. Eur. J. Clin. Microbiol. Infect. Dis. 20:329-333.
2. Alland, D., T. S. Whittam, M. B. Murray, M. D. Cave, M. H. Hazbon, K. Dix, M. Kokoris, A. Duesterhoeft, J. A. Eisen, C. M. Fraser, and R. D. Fleischmann. 2003. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J. Bacteriol. 185:3392-3399.
3. Ameyaw, M. M., F. Regateiro, T. Li, X. Liu, M. Tariq, A. Mobarek, N. Thornton, G. O. Folayan, J. Githang'a, A. Indalo, D. Ofori-Adjei, D. A. Price-Evans, and H. L. McLeod. 2001. MDR1 pharmacogenetics: frequency of the C3435T mutation in exon 26 is significantly influenced by ethnicity. Pharmacogenetics 11:217-221.
4. Ayyadevara, S., J. J. Thaden, and R. J. Shmookler Reis. 2000. Discrimination of primer 3′-nucleotide mismatch by taq DNA polymerase during polymerase chain reaction. Anal. Biochem. 284:11-18.
5. Bonnet, G., S. Tyagi, A. Libchaber, and F. R. Kramer. 1999. Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. USA 96:6171-6176.
6. Chee, M., R. Yang, E. Hubbell, A. Berno, X. C. Huang, D. Stern, J. Winkler, D. J. Lockhart, M. S. Morris, and S. P. Fodor. 1996. Accessing genetic information with high-density DNA arrays. Science 274:610-614.
7. El-Hajj, H. H., S. A. Marras, S. Tyagi, F. R. Kramer, and D. Alland. 2001. Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. J. Clin. Microbiol. 39:4131-4137.
8. Fan, X. Y., Z. Y. Hu, F. H. Xu, Z. Q. Yan, S. Q. Guo, and Z. M. Li. 2003. Rapid detection of rpoB gene mutations in rifampin-resistant Mycobacterium tuberculosis isolates in Shanghai by using the amplification refractory mutation system. J. Clin. Microbiol. 41:993-997.
9. Gutacker, M. M., J. C. Smoot, C. A. Migliaccio, S. M. Ricklefs, S. Hua, D. V. Cousins, E. A. Graviss, E. Shashkina, B. N. Kreiswirth, and J. M. Musser. 2002. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 162:1533-1543.
10. Hanna, G. J., V. A. Johnson, D. R. Kuritzkes, D. D. Richman, A. J. Brown, A. V. Savara, J. D. Hazelwood, and R. T. D'Aquila. 2000. Patterns of resistance mutations selected by treatment of human immunodeficiency virus type 1 infection with zidovadine, didanosine, and nevirapine. J. Infect. Dis. 181:904-911.
11. Kaboev, O. K., L. A. Luchkina, A. N. Tret'iakov, and A. R. Bahrmand. 2000. PCR hot start with primers with the structure of molecular beacons (hairpin-like structure). Nucleic Acids Res. 28:E94.
12. Kota, R., R. K. Varshney, T. Thiel, K. J. Dehmer, and A. Graner. 2001. Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145-151.
13. Lee, A. S., I. H. Lim, L. L. Tang, A. Telenti, and S. Y. Wong. 1999. Contribution of kasA analysis to detection of isoniazid-resistant Mycobacterium tuberculosis in Singapore. Antimicrob. Agents Chemother. 43:2087-2089.
14. Lee, L. G., K. J. Livak, B. Mullah, R. J. Graham, R. S. Vinayak, and T. M. Woudenberg. 1999. Seven-color, homogeneous detection of six PCR products. BioTechniques 27:342-349.
15. Martinez-Picado, J., K. Morales-Lopetegi, T. Wrin, J. G. Prado, S. D. Frost, C. J. Petropoulos, B. Clotet, and L. Ruiz. 2002. Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptions. AIDS 16:895-899.
16. Nazarenko, I., B. Lowe, M. Darfler, P. Ikonomi, D. Schuster, and A. Rashtchian. 2002. Multiplex quantitative PCR with self-quenched primers labeled with a single fluorophore. Nucleic Acids Res. 30:E37.
17. Newton, C. R., A. Graham, L. E. Heptinstall, S. J. Powell, C. Summers, N. Kalsheker, J. C. Smith, and A. F. Markham. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17:2503-2516.
18. Piatek, A. S., A. Telenti, M. R. Murray, H. El-Hajj, W. R. Jacobs, Jr., F. R. Kramer, and D. Alland. 2000. Genotypic analysis of Mycobacterium tuberculosis in two distinct populations with molecular beacons: implications for rapid susceptibility testing. Antimicrob. Agents Chemother. 44:103-110.
19. Piatek, A. S., S. Tyagi, A. C. Pol, A. Telenti, L. P. Miller, F. R. Kramer, and D. Alland. 1998. Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol. 16:359-363.
20. Ramaswamy, S., and J. M. Musser. 1998. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tuberc. Lung Dis. 79:3-29.
21. Ramaswamy, S. V., A. G. Amin, S. Goksel, C. E. Stager, S. J. Dou, H. El Sahly, S. L. Moghazeh, B. N. Kreiswirth, and J. M. Musser. 2000. Molecular genetic analysis of nucleotide polymorphisms associated with ethambutol resistance in human isolates of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 44:326-336.
22. Ramaswamy, S. V., R. Reich, S. J. Dou, L. Jasperse, X. Pan, A. Wanger, T. Quitugua, and E. A. Graviss. 2003. Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 47:1241-1250.
23. Redd, A. J., J. Roberts-Thomson, T. Karafet, M. Bamshad, L. B. Jorde, J. M. Naidu, B. Walsh, and M. F. Hammer. 2002. Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome. Curr. Biol. 12:673-677.
24. Saint-Joanis, B., H. Souchon, M. Wilming, K. Johnsson, P. M. Alzari, and S. T. Cole. 1999. Use of site-directed mutagenesis to probe the structure, function and isoniazid activation of the catalase/peroxidase, KatG, from Mycobacterium tuberculosis. Biochem. J. 338:753-760.
25. Sreevatsan, S., X. Pan, K. E. Stockbauer, N. D. Connell, B. N. Kreiswirth, T. S. Whittam, and J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94:9869-9874.
26. Suliman-Pollatschek, S., K. Kashkush, H. Shats, J. Hillel, and U. Lavi. 2002. Generation and mapping of AFLP, SSRs and SNPs in Lycopersicon esculentum. Cell. Mol. Biol. Lett. 7:583-597.
27. Tost, J., O. Brandt, F. Boussicault, D. Derbala, C. Caloustian, D. Lechner, and I. G. Gut. 2002. Molecular haplotyping at high throughput. Nucleic Acids Res. 30:E96.
28. Tyagi, S., D. P. Bratu, and F. R. Kramer. 1998. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16:49-53.
29. Tyagi, S., and F. R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308.
30. van Embden, J. D., M. D. Cave, J. T. Crawford, J. W. Dale, K. D. Eisenach, B. Giequel, P. Hermans, C. Martin, R. McAdam, T. M. Shinnick, et al. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:406-409.
31. Vignal, A., D. Milan, M. SanCristobal, and A. Eggen. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 34:275-305.
32. Wagenaar, T. R., V. T. Chow, C. Buranathai, P. Thawatsupha, and C. Grose. 2003. The out of Africa model of varicella-zoster virus evolution: single nucleotide polymorphisms and private alleles distinguish Asian clades from European/North American clades. Vaccine 21:1072-1081.
33. Waterfall, C. M., and B. D. Cobb. 2001. Single tube genotyping of sickle cell anaemia with PCR-based SNP analysis. Nucleic Acids Res. 29:E119.