A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas

Genome Research

Volumn 12, Issue 12, 2002, Pages 1935-1942

  Shagin, Dmitry A ^a,b   Rebrikov, Denis V ^a,b   Kozhemyako, Valery B ^c   Altshuler, Ilia M ^b   Shcheglov, Alex S ^a   Zhulidov, Pavel A ^a   Bogdanova, Ekaterina A ^a,b   Staroverov, Dmitry B ^b   Rasskazov, Valery A ^c   Lukyanov, Sergey ^a,b  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b Evrogen JSC   (Russian Federation)

^c PACIFIC INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

5 METHYLTETRAHYDROFOLIC ACID; DOUBLE STRANDED DNA; GENOMIC DNA; OLIGONUCLEOTIDE; PROTEIN P53; PROTHROMBIN; RNA; SINGLE STRANDED DNA;

CRAB; DNA CLEAVAGE; DNA DETERMINATION; DNA FINGERPRINTING; DNA PROBE; DNA RNA HYBRIDIZATION; DNA TEMPLATE; ENZYME SPECIFICITY; FLUORESCENCE ANALYSIS; GENE AMPLIFICATION; HEPATOPANCREAS; HETEROZYGOSITY; HOMOZYGOSITY; METHODOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SIGNAL DETECTION; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR SUPPRESSOR GENE;

ANIMALS; ANOMURA; CLONING, MOLECULAR; ENDONUCLEASES; LIVER; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HETERODUPLEXES; OLIGONUCLEOTIDES; PANCREAS; POLYMORPHISM, SINGLE NUCLEOTIDE; SUBSTRATE SPECIFICITY;

DECAPODA (CRUSTACEA); INVERTEBRATA; PARALITHODES CAMTSCHATICUS;

EID: 0036912415     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.547002     Document Type: Review

References (36)

1. Abarzua, P., LoSardo, J.E., Gubler, M.L., and Neri, A. 1995. Microinjection of monoclonal antibody PAb421 into human SW480 colorectal carcinoma cells restores the transcription activation function to mutant p53. Cancer Res. 55: 3490-3494.
2. Brookes, A.J. 1999. The essence of SNPs. Gene 234: 177-186.
3. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C.R., Lim, E.P., Kalyanaraman, N., et al. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22: 231-238.
4. Chomczynski, P. and Sacchi, N. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159.
5. Chou, M.Y. and Liao, T.H. 1990. Shrimp hepatopancreatic deoxyribonuclease-Purification and characterization as well as comparison with bovine pancreatic deoxyribonuclease. Biochim. Biophys. Acta. 1036: 95-100.
6. Friedhoff, P., Meiss, G., Kolmes, B., Pieper, U., Gimadutdinow, O., Urbanke, C., and Pingoud, A. 1996. Kinetic analysis of the cleavage of natural and synthetic substrates by the Serratia nuclease. Eur. J. Biochem. 241: 572-580.
7. Frosst P., Blom, H.J., Milos, R., Goyette, P., Sheppard, C.A., Matthews, R.G., Boers, G.J., den Heijer, M., Kluijtmans, L.A., van den Heuvel, L.P., et al. 1995. A candidate genetic risk factor for vascular disease: A common mutation in methylenetetrahydrofolate reductase. Nat. Genet. 10: 111-113.
8. Gite, S.U. and Shankar, V. 1995. Single-strand-specific nucleases. Crit. Rev. Microbiol. 21: 101-122.
9. Hacia, J.G., Fan, J.B., Ryder, O., Jin, L., Edgemon, K., Ghandour, G., Mayer, R.A., Sun, B., Hsie, L., Robbins, C.M., et al. 1999. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat. Genet. 22: 164-167.
10. Harlow, E. and Lane, D. 1988. Immunoblotting. Antibodies: Laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
11. Ho, H.C. and Liao, T.H. 1999. Protein structure and gene cloning of Syncephalastrum racemosum nuclease. Biochem. J. 339: 261-267.
12. Ho, HC., Shiau, P.F., Liu, F.C., Chung, J.G., and Chen, L.Y. 1998. Purification, characterization and complete amino acid sequence of nuclease C1 from Cunninghamella echinulata var. echinulata. Eur. J. Biochem. 256: 112-118.
13. Housman, D. and Ledley, F.D. 1998. Why pharmacogenomics? Why now? Nat. Biotechnol. 16: 492-493.
14. Jasin, M. 1996. Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet. 12: 224-228.
15. Kruglyak, L. 1997. The use of a genetic map of biallelic markers in linkage studies. Nat. Genet. 17: 21-24.
16. Kruglyak, L. 1999. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139-144.
17. Kunitz, M. 1950. Crystalline desoxyribonuclease. I. Isolation and general properties, spectrophotometric method for the measurement of desoxyribonuclease activity. II. Digestion of thymus nucleic acid (desoxyribonucleic acid). The kinetics of the reaction. J. Gen. Physiol. 33: 349-363.
18. Kwok, P.Y. 2000. High-throughput genotyping assay approaches. Pharmacogenomics 1: 95-100
19. Landegren, U., Nilsson, M., and Kwok, P.Y. 1998. Reading bits of genetic information: Methods for single-nucleotide polymorphism analysis. Genome Res. 8: 769-776.
20. Liao, T.-H. 1974. Bovine pancreatic deoxyribonuclease D. J. Biol. Chem. 249: 2354-2356.
21. Matz, M., Shagin, D., Bogdanova, E., Britanova, O., Lukyanov, S., Diatchenko, L., and Chenchik, A. 1999. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 27: 1558-1560.
22. McCarthy, J.J. and Hilfiker, R. 2000. The use of single-nucleotide polymorphism maps in pharmacogenomics. Nat. Biotechnol. 18: 505-S08.
23. Meiss, G., Franke, I., Gimadutdinow, O., Urbanke, C., and Pingoud, A. 1998. Biochemical characterization of Anabaena sp. strain PCC 7120 non-specific nuclease NucA and its inhibitor NuiA. Eur. J. Biochem. 251: 924-934.
24. 2+-dependent DNAase from sea urchin (Strongylocentrotus intermedius) embryos. Biokhimiia 46: 872-880.
25. Menzorova, N.I., Zinatulin, R.F., Favorov, V.V., and Rasskazov, V.A. 1993. Isolation and characterization of Ca,Mg-dependent endonuclease from hepatopancreas of Paralithodes Camchatika. Biokhimia 58: 681-691.
26. Nielsena, R. 2000. Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.
27. Poort, S.R., Rosendaal, F.R., Reitsma, P.H., and Bertina, R.M. 1996. A common genetic variation in the 3′ untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increase in venous thrombosis. Blood 88: 3698-3703.
28. Reddy, L.G. and Shankar, V. 1993. Immobilized nucleases. Crit. Rev. Biotechnol. 13: 255-273.
29. Risch, N. and Merikangas, K. 1996. The future of genetic studies of complex human diseases. Science 273: 1516-1517.
30. Roses, A.D. 2001. Pharmacogenetics. Hum. Mol. Genet. 10: 2261-2267.
31. Schultz, J., Copley, R.R., Doerks, T., Ponting, C.P., and Bork, P. 2000. SMART: A Web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28: 231-234.
32. Singwi, S. and Joshi, S. 2000. Potential nuclease-based strategies for HIV gene therapy. Front. Biosci. 5: D556-D579.
33. Suck, D. 1997. DNA recognition by structure-selective nucleases. Biopolymers 44: 405-421.
34. Syvanen, A.C. 2001. Accessing genetic variation: Genotyping single nucleotide polymorphisms. Nat. Rev. Genet. 2: 930-942.
35. Wang, W.Y., Liaw, S.H., and Liao, T.H. 2000. Cloning and characterization of a novel nuclease from shrimp hepatopancreas, and prediction of its active site. Biochem. J. 346: 799-804.
36. Williams, R.J. 2001. Restriction endonucleases and their uses. Methods Mol. Biol, 160: 409-429.