A novel single nucleotide polymorphism detection of a double-stranded DNA target by a ribonucleotide-carrying molecular beacon and thermostable RNase HII

Analytical Biochemistry

Volumn 398, Issue 1, 2010, Pages 83-92

  Liu, Xi Peng ^a   Hou, Jing Li ^a   Liu, Jian Hua ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

dsDNA target; Fluorescence detection; Molecular beacon; SNP genotyping; TthRNase HII

Indexed keywords

COST EFFECTIVENESS; DNA; DNA SEQUENCES; EFFICIENCY; FLUORESCENCE; NUCLEOTIDES; POLYMORPHISM;

COST-EFFECTIVE TECHNOLOGY; DOUBLE-STRANDED DNA (DS-DNA); FLUORESCENCE DETECTION; GENOTYPING; MOLECULAR BEACON; SINGLE NUCLEOTIDE POLYMORPHISM DETECTIONS; SINGLE NUCLEOTIDE POLYMORPHISMS; TTHRNASE HII;

GENE ENCODING;

DOUBLE STRANDED DNA; ESTERASE; HETERODUPLEX; HLA ANTIGEN; RIBONUCLEASE HII; RIBONUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA CLEAVAGE; DNA SEQUENCE; FLUORESCENCE; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HYBRIDIZATION; MOLECULAR BEACON; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; THERMOSTABILITY;

THERMUS THERMOPHILUS;

EID: 73549085174     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2009.10.042     Document Type: Article

References (29)

1. Bao Y.P., Huber M., Wei T.F., Marla S.S., Storhoff J.J., and Muller U.R. SNP identification in unamplified human genomic DNA with gold nanoparticle probes. Nucleic Acids Res. 33 (2005) e15
2. Kim S., and Misra A. SNP genotyping: technologies and biomedical applications. Annu. Rev. Biomed. Eng. 9 (2007) 289-320
3. Prince J.A., Feuk L., Howell W.M., Jobs M., Emahazion T., Blennow K., and Brookes A.J. Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. Genome Res. 11 (2001) 152-162
4. Ahmadian A., Gharizadeh B., O'Meara D., Odeberg J., and Lundeberg J. Genotyping by apyrase-mediated allele-specific extension. Nucleic Acids Res. 29 (2001) e121
5. Khanna M., Park P., Zirvi M., Cao W., Picon A., Day J., Paty P., and Barany F. Multiplex PCR/LDR for detection of K-ras mutations in primary colon tumors. Oncogene 18 (1999) 27-38
6. Ichinose H., Kitaoka M., Okamura N., Maruyama T., Kamiya N., and Goto M. Detection of single-base mutations by fluorogenic ribonuclease protection assay. Anal. Chem. 77 (2005) 7047-7053
7. Krebs S., Medugorac I., Seichter D., and Forster M. RNaseCut: a MALDI mass spectrometry-based method for SNP discovery. Nucleic Acids Res. 31 (2003) e37
8. Myers R.M., Larin Z., and Maniatis T. Detection of single base substitutions by ribonuclease cleavage at mismatches in RNA:DNA duplexes. Science 230 (1985) 1242-1246
9. Oleykowski C.A., Bronson Mullins C.R., Godwin A.K., and Yeung A.T. Mutation detection using a novel plant endonuclease. Nucleic Acids Res. 26 (1998) 4597-4602
10. Till B.J., Burtner C., Comai L., and Henikoff S. Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res. 32 (2004) 2632-2641
11. Yeung A.T., Hattangadi D., Blakesley L., and Nicolas E. Enzymatic mutation detection technologies. Biotechniques 38 (2005) 749-758
12. + proofreading polymerases mediate genetic analysis and its application in biomedical studies. Acta Pharmacol. Sin. 26 (2005) 302-306
13. Gao H., Huang J., Barany F., and Cao W. Switching base preferences of mismatch cleavage in endonuclease: V. An improved method for scanning point mutations. Nucleic Acids Res. 35 (2007) e2
14. Shagin D.A., Rebrikov D.V., Kozhemyako V.B., Altshuler I.M., Shcheglov A.S., Zhulidov P.A., Bogdanova E.A., Staroverov D.B., Rasskazov V.A., and Lukyanov S. A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res. 12 (2002) 1935-1942
15. Goldrick M.M. RNase cleavage-based methods for mutation/SNP detection, past and present. Hum. Mutat. 18 (2001) 190-204
16. Ohtani N., Haruki M., Morikawa M., and Kanaya S. Molecular diversities of RNases H. J. Biosci. Bioeng. 88 (1999) 12-19
17. 2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families. Biochemistry 38 (1999) 605-618
18. Kanaya S., and Ikehara M. Functions and structures of ribonuclease H enzymes. Subcell. Biochem. 24 (1995) 377-422
19. Sato A., Kanai A., Itaya M., and Tomita M. Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus. Biochem. Biophys. Res. Commun. 309 (2003) 247-252
20. Haruki M., Tsunaka Y., Morikawa M., and Kanaya S. Cleavage of a DNA-RNA-DNA/DNA chimeric substrate containing a single ribonucleotide at the DNA-RNA junction with prokaryotic RNases HII. FEBS Lett. 531 (2002) 204-208
21. Pei D., Liu J., Liu X., and Li S. Expression of both Chlamydia pneumoniae RNase HIIs in Escherichia coli. Protein Expr. Purif. 40 (2005) 101-106
22. Hou J., Liu X., Pei D., and Liu J. RNase HII from Chlamydia pneumoniae discriminates mismatches incorporation into DNA-rN1-DNA/DNA duplexes. Biochem. Biophys. Res. Commun. 356 (2007) 988-992
23. Tyagi S., and Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14 (1996) 303-308
24. Zheleznaya L.A., Kopein D.S., Rogulin E.A., Gubanov S.I., and Matvienko N.I. Significant enhancement of fluorescence on hybridization of a molecular beacon to a target DNA in the presence of a site-specific DNA nickase. Anal. Biochem. 348 (2006) 123-126
25. Nikiforov T.T., Rendle R.B., Kotewicz M.L., and Rogers Y.H. The use of phosphorothioate primers and exonuclease hydrolysis for the preparation of single-stranded PCR products and their detection by solid-phase hybridization. PCR Methods Appl. 3 (1994) 285-291
26. Hou J., Liu X., Wang J., Liu J., and Duan T. Molecular beacons for isothermal fluorescence enhancement by the cleavage of RNase HII from Chlamydia pneumoniae. Anal. Biochem. 371 (2007) 162-166
27. Barker C.S., Griffin C., Dolganov G.M., Hanspers K., Yang J.Y., and Erle D.J. Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics 6 (2005) 57
28. Ono N., Suzuki S., Furusawa C., Agata T., Kashiwagi A., Shimizu H., and Yomo T. An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. Bioinformatics 24 (2008) 1278-1285
29. Olivier M., Chuang L.M., Chang M.S., Chen Y.T., Pei D., Ranade K., de Witte A., Allen J., Tran N., Curb D., Pratt R., Neefs H., de Arruda Indig M., Law S., Neri B., Wang L., and Cox D.R. High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucleic Acids Res. 30 (2002) e53