Application of Blocking Oligonucleotides to Improve Signal-to-Noise Ratio in a PCR

Methods in Molecular Biology

Volumn 687, Issue , 2011, Pages 265-274

  Vestheim, Hege ^a   Deagle, Bruce E ^b   Jarman, Simon N ^c  

^a UNIVERSITY OF BERGEN   (Norway)

^b UNIVERSITY OF VICTORIA   (Canada)

^c AUSTRALIAN ANTARCTIC DIVISION   (Australia)

Author keywords

Allele specific competitive blocker PCR; Blocking oligonucleotide; Blocking primers; Blocking probes; C3 spacer, peptide nucleic acids; Competitive probes; Enhanced amplification of rare sequences; Locked nucleic acids

Indexed keywords

OLIGONUCLEOTIDE; PRIMER DNA;

ARTICLE; CHEMISTRY; METHODOLOGY; POLYMERASE CHAIN REACTION;

DNA PRIMERS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION;

MLCS; MLOWN;

EID: 79952276747     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-944-4_19     Document Type: Chapter

References (29)

1. Bensch, S., Pérez-Tris, J., Waldenström, J., and Hellgren, O. (2004) Linkage between nuclear and mitochondrial DNA sequences in avian malaria parasites: multiple cases of cryptic speciation? Evolution 58, 1617–21.
2. Sidransky, D. (1997) Nucleic acid-based methods for the detection of cancer. Science 278, 1054–58.
3. Deagle, B. E., Kirkwood, R., and Jarman, S. N. (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology 18, 2022–38.
4. von Wintzingerode, F., Gobel, U. B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews 21, 213–29.
5. Polz, M. F. and Cavanaugh, C. M. (1998) Bias in template-to-product ratios in multi-template PCR. Applied and Environmental Microbiology 64, 3724–30.
6. King, R. A., Read, D. S., Traugott, M., and Symondson, W. O. C. (2008) Molecular analysis of predation: a review of best practice for DNA-based approaches. Molecular Ecology 17, 947–63.
7. Deagle, B. E., Eveson, J. P., and Jarman, S. N. (2006) Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces. Frontiers in Zoology 3, 11.
8. Parsons, B. L. and Heflich, R. H. (1998) Detection of a mouse H-ras codon 61 mutation using a modified allele-specific competitive blocker PCR genotypic selection method. Mutagenesis 13, 581–8.
9. Carlson, C. M., Dupuy, A., Fritz, S., Roberg-Perez, K., Fletcher, C. F., and Largaespada, D. A. (2003) Transposon mutagenesis of the mouse germline. Genetics 165, 243–56.
10. Corless, C. L., Harrell, P., Lacouture, M., Bainbridge, T., Le, C., Gatter, K., White, C., Granter, S., and Heinrich, M. C. (2006) Allele-specific polymerase chain reaction for the imatinib-resistant KIT D816V and D816F mutations in mastocytosis and acute myelog-enous leukaemia. Journal of Molecular Diagnostics 8, 604–12.
11. Vestheim, H. and Jarman, S. N. (2008) Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology 5, 12.
12. Peano, C., Lesignoli, F., Gulli, M., Corradini, R., Samson, M. C., Marchelli, R., and Marmiroli, N. (2005) Development of a peptide nucleic acid polymerase chain reaction clamping assay for semiquantitative evaluation of genetically modified organism content in food. Analytical Biochemistry 344, 174–82.
13. Karkare, S. and Bhatnagar, D. (2006) Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino. Applied Microbiology and Biotechnology 71, 575–86.
14. Tatsumi, K., Mitani, Y., Watanabe, J., Takakura, H., Hoshit, K., Kawai, Y., Kikuchi, T., Kogo, Y., Oguchi-Katayama, A., Tomaru, Y., Kanamori, H., Baba, M., Ishidao, T., Usui, K., Itoh, M., Cizdziel, P. E., Lezhava, A., Ueda, M., Ichikawa, Y., Endo, I., Togo, S., Shimada, H., and Hayashizaki, Y. (2008) Rapid screening assay for KRAS mutations by the modified smart amplification process. Journal of Molecular Diagnostics 10, 520–6.
15. Ørum H. (2000) PCR clamping. Current Issues in Molecular Biology, 1, 27–30.
16. Troedsson, C., Lee, R. F., Walters, T., Stokes, V., Brinkley, K., Naegele, V., and Frischer, M. E. (2008) Detection and discovery of crustacean parasites in blue crabs (Callinectes sapi-dus) by using 18S rRNA gene-targeted denaturing high-performance liquid chromatography. Applied and Environmental Microbiology 74, 4346–53.
17. Egholm, M., Buchardt, O., Christensen, L., Behrens, C., Freier, S. M., Driver, D. A., Berg, R. H., Kim, S. K., Norden, B., and Nielsen, P. E. (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365, 566–8.
18. Ørum, H., Nielsen, P. E., Egholm, M., Berg, R. H., Buchardt, O., and Stanley, C. (1993) Single-base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Research 21, 5332–6.
19. Dominguez P. L. and Kolodney M. S. (2005) Wild-type blocking polymerase chain reaction for detection of single nucleotide minority mutations from clinical specimens. Oncogene 24, 6830–4.
20. Lawyer, F. C., Stoffel, S., Saiki, R. K., Chang, S. Y., Landre, P. A., Abramson, R. D., and Gelfand, D. H. (1993) High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5’ to 3’ exonuclease activity. PCR Methods and Applications 2, 275–87.
21. Yu, D., Mukai, M., Liu, Q., and Steinman, C. R. (1997) Specific inhibition of PCR by non-extendable oligonucleotides using a 5’ to 3’ exonuclease-deficient DNA polymerase. BioTechniques 23, 714–20.
22. Dieffenbach, C. W., Lowe, T. M. J., and Dveksler, G. S. (1993) General concepts for PCR primer design. PCR-Methods and Applications 3, S30–7.
23. Chun, J. Y., Kim, K. J., Hwang, I. T., Kim, Y. J., Lee, D. H., Lee, I. K., and Kim, J. K. (2007) Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene. Nucleic Acids Research 35, e40.
24. von Wintzingerode, F., Landt, O., Ehrlich, A., and Gobel, U. B. (2000) Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity. Applied and Environmental Microbiology 66, 549–57.
25. Smalla, K., Oros-Sichler, M., Milling, A., Heuer, H., Baumgarte, S., Becker, R., Neuber, G., Kropf, S., Ulrich, A., and Tebbe, C. C. (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results? Journal of Microbiological Methods 69, 470–9.
26. Muyzer, G. (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Current Opinion in Microbiology 2, 317–22.
27. Robinson, B. S., Monis, P. T., and Dobson, P. J. (2006) Rapid, sensitive, and discriminating identification of Naegleria spp. by real-time PCR and melting-curve analysis. Applied and Environmental Microbiology 72, 5857–63.
28. De Jong, W., De Jong, D., and Bodis, M. (2003) A fluorogenic 5’ nuclease (TaqMan) assay to assess dosage of a marker tightly linked to red skin color in autotetraploid potato. Theoretical and Applied Genetics 107, 1384–90.
29. Dunshea, G., Barros, N., Wells, R., Gales, N., Hindell, M., and Jarman, S. (2008) Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system. Bulletin of Entomological Research 98, 239–48.