Enhancing allele-specific PCR for specifically detecting short deletion and insertion DNA mutations

Molecular and Cellular Probes

Volumn 24, Issue 1, 2010, Pages 15-19

  Wang, Yiran ^a   Rollin, Joseph A ^a   Percival Zhang, Y H ^a  

^a State University   (United States)

Author keywords

3 Terminal nucleotide; Allele specific PCR; Deletion mutation; Insertion mutation; Mismatch; Mutagenesis

Indexed keywords

DNA; PLASMID DNA;

3' UNTRANSLATED REGION; ACCURACY; ARTICLE; BASE MISPAIRING; CONTROLLED STUDY; DNA TEMPLATE; GENE AMPLIFICATION; GENE DELETION; GENE EXPRESSION REGULATION; GENE INSERTION; GENE MUTATION; MUTATIONAL ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RELIABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; SITE DIRECTED MUTAGENESIS;

ALLELES; BASE PAIR MISMATCH; MODELS, GENETIC; MUTAGENESIS, INSERTIONAL; MUTAGENESIS, SITE-DIRECTED; POLYMERASE CHAIN REACTION; SEQUENCE DELETION;

EID: 73449098535     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcp.2009.08.001     Document Type: Article

References (48)

1. Kwok P.Y. Methods for genotyping single nucleotide polymorphisms. Annu Rev Genomics Hum Genet 2 (2001) 235-258
2. Newton C.R., Graham A., Heptinstall L.E., Powell S.J., Summers C., Kalsheker N., et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17 (1989) 2503-2516
3. Ayyadevara S., Thaden J.J., and Shmookler Reis R.J. Discrimination of primer 3-nucleotide mismatch by taq DNA polymerase during polymerase chain reaction. Anal Biochem 284 (2000) 11-18
4. Huang M.M., Arnheim N., and Goodman M.F. Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR. Nucleic Acids Res 20 (1992) 4567-4573
5. Walsh P.S., Erlich H.A., and Higuchi R. Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl 1 (1992) 241-250
6. Hultin E., Kaller M., Ahmadian A., and Lundeberg J. Competitive enzymatic reaction to control allele-specific extensions. Nucleic Acids Res 33 (2005) e48
7. Kwok S., Kellogg D.E., McKinney N., Spasic D., Goda L., Levenson C., et al. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res 18 (1990) 999-1005
8. Fu Q., Ruegger P., Bent E., Chrobak M., and Bomeman J. PRISE (PRImer SElector): software for designing sequence - selective PCR primers. J Microbiol Methods 72 (2008) 263-267
9. Wangkumhang P., Chaichoompu K., Ngamphiw C., Ruangrit U., Chanprasert J., Assawamakin A., et al. WASP: a web-based allele-specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics 8 (2007) 275
10. Chang H.W., Chuang L.Y., Cheng Y.H., Hung Y.C., Wen C.H., Gu D.L., et al. Prim-SNPing: a primer designer for cost-effective SNP genotyping. BioTechniques 46 (2009) 421-431
11. Fortina P., Conant R., Parrella T., Rappaport E., Scanlin T., Schwartz E., et al. Fluorescence-based, multiplex allele-specific PCR (MASPCR) detection of the delta F508 deletion in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Mol Cell Probes 6 (1992) 353-356
12. Mitrecic D., Mavric S., and Gajovic S. PCR-based identification of short deletion/insertions and single nucleotide substitutions in genotyping of splotch (Pax3sp) and truncate (Nototc) mouse mutants. Mol Cell Probes 22 (2008) 110-114
13. Rizzo W.B., Carney G., and De Laurenzi V. A common deletion mutation in European patients with Sjögren-Larsson syndrome. Biochem Mol Med 62 (1997) 178-181
14. Lucotte G., Bathelier C., and Champenois T. PCR test for diagnosis of the common GJB2 (connexin 26) 35delG mutation on dried blood spots and determination of the carrier frequency in France. Mol Cell Probes 15 (2001) 57-59
15. Yamakawa K., Morita R., Takahashi E., Hori T., Ishikawa J., and Nakamura Y. A detailed deletion mapping of the short arm of chromosome-3 in sporadic renal-cell carcinoma. Cancer Res 51 (1991) 4707-4711
16. Steen V.M., Andreassen O.A., Daly A.K., Tefre T., Borresen A.L., Idle J.R., et al. Detection of the poor metabolizer-associated Cyp2d6(D) gene deletion allele by long-PCR technology. Pharmacogenetics 5 (1995) 215-223
17. Yoshida H., Mitarai T., Kawamura T., Kitajima T., Miyazaki Y., Nagasawa R., et al. Role of the deletion polymorphism of the angiotensin-converting enzyme gene in the progression and therapeutic responsiveness of Iga nephropathy. J Clin Invest 96 (1995) 2162-2169
18. Danser A.H.J., Schalekamp M.A.D.H., Bax W.A., Vandenbrink A.M., Saxena P.R., Riegger G.A.J., et al. Angiotensin-converting enzyme in the human heart - effect of the deletion insertion polymorphism. Circulation 92 (1995) 1387-1388
19. Cambien F., Poirier O., Lecerf L., Evans A., Cambou J.P., Arveiler D., et al. Deletion polymorphism in the gene for angiotensin-converting enzyme is a potent risk factor for myocardial-infarction. Nature 359 (1992) 641-644
20. Midorikawa Y., Yamamoto S., Tsuji S., Kamimura N., Ishikawa S., Igarashi H., et al. Allelic imbalances and homozygous deletion on 8p23.2 for stepwise progression of hepatocarcinogenesis. Hepatology 49 (2009) 513-522
21. Crescenti A., Gasso P., Mas S., Abellana R., Deulofeu R., Parellada E., et al. Insertion/deletion polymorphism of the angiotensin-converting enzyme: gene is associated with schizophrenia in a Spanish population. Psychiatry Res 165 (2009) 175-180
22. Vallejo M., Martinez-Palomino G., Ines-Real S., Perez-Hernandez N., Juarez-Rojas J.G., and Vargas-Alarcon G. Relationship between the angiotensin I-converting enzyme insertion/deletion (I/D) polymorphism and cardiovascular risk factors in healthy young Mexican women. Genet Test Mol Biomarkers 13 (2009) 237-242
23. Decker R.A., and Collins F.S. Dinucleotide repeat polymorphism at the D10s469 locus. Hum Mol Genet 2 (1993) 1330
24. Tagle D.A., Blanchardmcquate K.L., Valdes J., Castilla L., Macdonald M.E., Gusella J.F., et al. Dinucleotide repeat polymorphism in the Huntingtons-disease region at the D4s182 locus. Hum Mol Genet 2 (1993) 489
25. Grobbelaar J.J., Oosthuizen C.J., and Kotze M.J. Screening South African familial adenomatous polyposis families for the five-nucleotide deletion at codon 1309 of the APC gene. Mol Cell Probes 9 (1995) 49-51
26. Hutchison III C.A., Phillips S., Edgell M.H., Gillam S., Jahnke P., and Smith M. Mutagenesis at a specific position in a DNA sequence. J Biol Chem 253 (1978) 6551-6560
27. Rothlisberger D., Khersonsky O., Wollacott A.M., Jiang L., DeChancie J., Betker J., et al. Kemp elimination catalysts by computational enzyme design. Nature 453 (2008) 190-195
28. Villafranca J.E., Howell E.E., Voet D.H., Strobel M.S., Ogden R.C., Abelson J.N., et al. Directed mutagenesis of dihydrofolate reductase. Science 222 (1983) 782-788
29. Wang Y., and Zhang Y- H.P. A highly active phosphoglucomutase from clostridium thermocellum: cloning, purification, characterization, and enhanced thermostability. J Appl Microbiol (2009) 10.1111/j.1365-2672.2009.04396.x
30. Wang Y., and Zhang Y.-H.P. Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration. Microb Cell Fact 8 (2009) 30
31. Kramer B., Kramer W., and Fritz H.J. Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Cell 38 (1984) 879-887
32. Zheng L., Baumann U., and Reymond J.L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 32 (2004) e115
33. Piechocki M.P., and Hines R.N. Oligonucleotide design and optimized protocol for site-directed mutagenesis. BioTechniques 16 (1994) 702-707
34. Wu W., Jia Z.C., Liu P., Xie Z.G., and Wei Q. A novel PCR strategy for high-efficiency, automated site-directed mutagenesis. Nucleic Acids Res 33 (2005) e110
35. Chiu J., March P.E., Lee R., and Tillett D. Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h. Nucleic Acids Res 32 (2004) e174
36. Ho S.N., Hunt H.D., Horton R.M., Pullen J.K., and Pease L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77 (1989) 51-59
37. Kunkel T.A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A 82 (1985) 488-492
38. Tyagi R., Lai R., and Duggleby R.G. A new approach to 'megaprimer' polymerase chain reaction mutagenesis without an intermediate gel purification step. BMC Biotechnol 4 (2004) 2
39. Rashtchian A., Thornton C.G., and Heidecker G. A novel method for site-directed mutagenesis using PCR and uracil DNA glycosylase. PCR Methods Appl 2 (1992) 124-130
40. Smith M. In vitro mutagenesis. Annu Rev Genet 19 (1985) 423-462
41. Woodyer R., Simurdiak M., van der Donk W.A., and Zhao H. Heterologous expression, purification, and characterization of a highly active xylose reductase from Neurospora crassa. Appl Environ Microbiol 71 (2005) 1642-1647
42. Newton C.R., Heptinstall L.E., Summers C., Super M., Schwarz M., Anwar R., et al. Amplification refractory mutation system for prenatal diagnosis and carrier assessment in cystic fibrosis. Lancet 2 (1989) 1481-1483
43. Rizzo W.B., and Carney G. Sjögren-Larsson syndrome: diversity of mutations and polymorphisms in the fatty aldehyde dehydrogenase gene (ALDH3A2). Hum Mutat 26 (2005) 1-10
44. Pearson S.L., and Hessner M.J. A(1,2)BO(1,2) genotyping by multiplexed allele-specific PCR. Br J Haematol 100 (1998) 229-234
45. Syvanen A.C. Toward genome-wide SNP genotyping. Nat Genet 37 Suppl. (2005) S5-S10
46. Wang Y., Stanzel M., Gumbrecht W., Humenik M., and Sprinzl M. Esterase 2-oligodeoxynucleotide conjugates as sensitive reporter for electrochemical detection of nucleic acid hybridization. Biosens Bioelectron 22 (2007) 1798-1806
47. Patolsky F., Lichtenstein A., and Willner I. Detection of single-base DNA mutations by enzyme-amplified electronic transduction. Nat Biotechnol 19 (2001) 253-257
48. Qiu P., Shandilya H., and Gerard G.F. A method for clone sequence confirmation using a mismatch-specific DNA endonuclease. Mol Biotechnol 29 (2005) 11-18