Masking oligonucleotides improve sensitivity of mutation detection based on guanine quenching

Analytical Biochemistry

Volumn 354, Issue 1, 2006, Pages 8-14

  Maruyama, Tatsuo ^a   Shinohara, Toshimitsu ^a   Hosogi, Takuya ^a   Ichinose, Hirofumi ^b   Kamiya, Noriho ^a   Goto, Masahiro ^a,b  

^a Graduate School of Engineering   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

DNA; Fluorescence resonance energy transfer; Fluorescent dye; Guanine quenching; Single nucleotide polymorphisms

Indexed keywords

DNA; ENERGY TRANSFER; FLUORESCENCE; OLIGONUCLEOTIDES; QUENCHING; VIRUSES;

DNA OLIGONUCLEOTIDES; DNA POLYMERASE GENES; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; GUANINE QUENCHING; HEPATITIS B VIRUS; MUTATION DETECTION; SINGLE NUCLEOTIDE POLYMORPHISMS;

POSITIVE IONS;

DNA; DNA POLYMERASE; GUANINE; OLIGONUCLEOTIDE;

ARTICLE; FLUORESCENCE; HEPATITIS DELTA VIRUS; HUMAN; METHODOLOGY; POINT MUTATION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; VIRUS GENE; WILD TYPE;

HEPATITIS B VIRUS;

EID: 33744531012     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.03.056     Document Type: Article

References (29)

1. Pettipher R., and Cardon L.R. The application of genetics to the discovery of better medicines. Pharmacogenomics 3 (2002) 257-263
2. Sachidanandam R., Weissman D., Schmidt S.C., Kakol J.M., Stein L.D., Marth G., Sherry S., Mullikin J.C., Mortimore B.J., Willey D.L., Hunt S.E., Cole C.G., Coggill P.C., Rice C.M., Ning Z., Rogers J., Bentley D.R., Kwok P.Y., Mardis E.R., Yeh R.T., Schultz B., Cook L., Davenport R., Dante M., Fulton L., Hillier L., Waterston R.H., McPherson J.D., Gilman B., Schaffner S., Van Etten W.J., Reich D., Higgins J., Daly M.J., Blumenstiel B., Baldwin J., Stange-Thomann N., Zody M.C., Linton L., Lander E.S., and Altshuler D. International SNP Map Working Group, A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 (2001) 928-933
3. Chin R., and Locarnini S. Treatment of chronic hepatitis B: Current challenges and future directions. Rev. Med. Virol. 13 (2003) 255-272
4. Tipples G.A., Ma M.M., Fischer K.P., Bain V.G., Kneteman N.M., and Tyrrell D.L.J. Mutation in HBV RNA-dependent DNA polymerase confers resistance to lamivudine in vivo. Hepatology 24 (1996) 714-717
5. Wang J., Palecek E., Nielsen P.E., Rivas G., Cai X.H., Shiraishi H., Dontha N., Luo D.B., and Farias P.A.M. Peptide nucleic acid probes for sequence-specific DNA biosensors. J. Am. Chem. Soc. 118 (1996) 7667-7670
6. Schafer A.J., and Hawkins J.R. DNA variation and the future of human genetics. Nat. Biotechnol. 16 (1998) 33-39
7. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270 (1995) 467-470
8. Ross P.L., Lee K., and Belgrader P. Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry. Anal. Chem. 69 (1997) 4197-4202
9. Gilles P.N., Wu D.J., Foster C.B., Dillon P.J., and Chanock S.J. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat. Biotechnol. 17 (1999) 365-370
10. Shalon D., Smith S.J., and Brown P.O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6 (1996) 639-645
11. Dubertret B., Calame M., and Libchaber A.J. Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat. Biotechnol. 19 (2001) 365-370
12. Schena M. DNA Microarrays (1999), Oxford University Press, New York
13. Guo Z., Liu Q.H., and Smith L.M. Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization. Nat. Biotechnol. 15 (1997) 331-335
14. Boon E.M., Ceres D.M., Drummond T.G., Hill M.G., and Barton J.K. Mutation detection by electrocatalysis at DNA-modified electrodes. Nat. Biotechnol. 18 (2000) 1096-1100
15. Livak K.J., Marmaro J., and Todd J.A. Towards fully automated genome-wide polymorphism screening. Nat. Genet. 4 (1995) 341-342
16. Piatek A., Piatek A.S., Tyagi S., Pol A.C., Telenti A., Miller L.P., Kramer F.R., and Alland D. Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol. 16 (1998) 359-363
17. Tyagi S., Bratu D.P., and Kramer F.R. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16 (1998) 49-53
18. Chen X., Zehnbauer B., Gnirke A., and Kwok P.Y. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc. Natl. Acad. Sci. USA 94 (1997) 10756-10761
19. Hall J.G., Eis P.S., Law S.M., Reynaldo L.P., Prudent J.R., Marshall D.J., Allawi H.T., Mast A.L., Dahlberg J.E., Kwiatkowski R.W., de Arruda M., Neri B.P., and Lyamichev V.I. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl. Acad. Sci. USA 97 (2000) 8272-8277
20. Myakishev M.V., Khripin Y., Hu S., and Hamer D.H. High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res. 11 (2001) 163-169
21. Cooper J.P., and Hagerman P.J. Analysis of fluorescence energy-transfer in duplex and branched DNA-molecules. Biochemistry 29 (1990) 9261-9268
22. Lee S.P., Porter D., Chirikjian J.G., Knutson J.R., and Han M.K. A fluorometric assay for DNA cleavage reactions characterized with BamHI restriction endonuclease. Anal. Biochem. 220 (1994) 377-383
23. Walter N.G., and Burke J.M. Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates. RNA 3 (1997) 392-404
24. Horn T., Chang C.A., and Urdea M.S. Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays. Nucleic Acids Res. 25 (1997) 4842-4849
25. Draganescu A., Hodawadekar S.C., Gee K.R., and Brenner C. Fhit-nucleotide specificity probed with novel fluorescent and fluorogenic substrates. J. Biol. Chem. 275 (2000) 4555-4560
26. Torimura M., Kurata S., Yamada K., Yokomaku T., Kamagata Y., Kanagawa T., and Kurane R. Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base. Anal. Sci. 17 (2001) 155-160
27. Kurata S., Kanagawa T., Yamada K., Torimura M., Yokomaku T., Kamagata Y., and Kurane R. Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY FL-labeled probe or primer. Nucleic Acids Res. 29 (2001) e34
28. Maruyama T., Takata T., Ichinose H., Kamiya N., Kuma H., Hamasaki N., Morita H., and Goto M. Detection of point mutations in the HBV polymerase gene using a fluorescence intercalator in reverse micelles. Biotechnol. Prog. 21 (2005) 575-579
29. Maruyama T., Shinohara T., Ichinose H., Kitaoka M., Okamura N., Kamiya N., and Goto M. Mutation detection in DNA oligonucleotides based on a guanine quenching method coupled with enzymatic digestion of single-stranded DNA. Biotechnol. Lett. 27 (2005) 1349-1354