Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting

Journal of Molecular Diagnostics

Volumn 9, Issue 3, 2007, Pages 284-289

  Seipp, Michael T ^a   Durtschi, Jacob D ^a   Liew, Michael A ^a   Williams, Jamie ^b   Damjanovich, Kristy ^a   Pont Kingdon, Genevieve ^a   Lyon, Elaine ^a,b,c   Voelkerding, Karl V ^a,c   Wittwer, Carl T ^a,b,c  

^a ARUP INSTITUTE FOR CLINICAL AND EXPERIMENTAL PATHOLOGY   (United States)

^b ARUP LABORATORIES   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

AMPLICON; ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; DNA ISOLATION; GENOTYPE; HIGH TEMPERATURE; HOMOZYGOSITY; HYBRIDIZATION; LOW TEMPERATURE; MUTANT; NUCLEOTIDE SEQUENCE; TEMPERATURE;

EID: 34547639077     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2007.060136     Document Type: Article

References (23)

1. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ: High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 2003, 49:853-860
2. Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C: Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 2004, 50:1156-1164
3. Graham R, Liew M, Meadows C, Lyon E, Wittwer CT: Distinguishing different DNA heterozygotes by high-resolution melting. Clin Chem 2005, 51:1295-1298
4. Palais RA, Liew MA, Wittwer CT: Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping. Anal Biochem 2005, 346:167-175
5. Reed GH, Wittwer CT: Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 2004, 50:1748-1754
6. Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, Behlke MA, Walder JA: Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 2004, 43:3537-3554
7. Rouzina I, Bloomfield VA: Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects. Biophys J 1999, 77:3252-3255
8. Rouzina I, Bloomfield VA: Heat capacity effects on the melting of DNA. 1. General aspects. Biophys J 1999, 77:3242-3251
9. Wolfe AR, Meehan T: The effect of sodium ion concentration on intrastrand base-pairing in single-stranded DNA. Nucleic Acids Res 1994, 22:3147-3150
10. Gundry CN, Vandersteen JG, Reed GH, Pryor RJ, Chen J, Wittwer CT: Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin Chem 2003, 49:396-406
11. Bernard PS, Lay MJ, Wittwer CT: Integrated amplification and detection of the C677T point mutation in the methylenetetrahydrofolate reductase gene by fluorescence resonance energy transfer and probe melting curves. Anal Biochem 1998, 255:101-107
12. Wittwer CT, Herrmann MG, Gundry CN, Elenitoba-Johnson KS: Real-time multiplex PCR assays. Methods 2001, 25:430-442
13. van der Put NM, Gabreels F, Stevens EM, Smeitink JA, Trijbels FJ, Eskes TK, van den Heuvel LP, Biota HJ: A second common mutation in the methylenetetrahydrofolate reductase gene: an additional risk factor for neural-tube defects? Am J Hum Genet 1998, 62:1044-1051
14. Cradic KW, Wells JE, Allen L, Kruckeberg KE, Singh RJ, Grebe SK: Substitution of 3′-phosphate cap with a carbon-based blocker reduces the possibility of fluorescence resonance energy transfer probe failure in real-time PCR assays. Clin Chem 2004, 50:1080-1082
15. Chou LS, Meadows C, Wittwer CT, Lyon E: Unlabeled oligonucleotide probes modified with locked nucleic acids for improved mismatch discrimination in genotyping by melting analysis. Biotechniques' 2005, 39:644-648
16. Erali M, Palais R, Wittwer CT: SNP genotyping by unlabeled probe melting analysis. Methods in Molecular Biology. Edited by O Seitz, A Marx. Totowa, Humana Press, 2006
17. Bernard PS, Ajioka RS, Kushner JP, Wittwer CT: Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes. Am J Pathol 1998, 153:1055-1061
18. Kutyavin IV, Afonina IA, Mills A, Gorn VV, Lukhtanov EA, Belousov ES, Singer MJ, Walburger DK, Lokhov SG, Gall AA, Dempcy R, Reed MW, Meyer RB, Hedgpeth J: 3′-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res 2000, 28:655-661
19. Tyagi S, Bratu DP, Kramer FR: Multicolor molecular beacons for allele discrimination. Nat Biotechnol 1998, 16:49-53
20. Zhou L, Myers AN, Vandersteen JG, Wang L, Wittwer CT: Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye. Clin Chem 2004, 50:1328-1335
21. Herrmann MG, Durtschi JD, Bromley LK, Wittwer CT, Voelkerding KV: Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin Chem 2006, 52:494-503
22. von Ahsen N: Two for typing: homogeneous combined single-nucleotide polymorphism scanning and genotyping. Clin Chem 2005, 51:1761-1762
23. Volcik KA, Blanton SH, Northrup H: Examinations of methylenetetrahydrofolate reductase C677T and A1298C mutations - and in utero viability. Am J Hum Genet 2001, 69:1150-1153