Scanning for DNA variants by denaturant capillary electrophoresis

Methods in Molecular Biology

Volumn 439, Issue , 2008, Pages 19-34

  Ekstrøm, Per O ^a  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

CDCE (constant denaturant capillary electrophoresis); CTCE (cycling temperature capillary electrophoresis); DGGE (denaturant gradient gel electrophoresis); DsDNA double strand DNA; PCR (polymerase chain reaction); SsDNA single strand DNA

Indexed keywords

EID: 84934438255     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-188-8_2     Document Type: Article

References (42)

1. Watson J, Crick F (1953) Molecular structure of nucleic acids - a structure for deoxyribose nucleic acid. Nature 171:737-738
2. Kleppe K, Ohtsuka E, Kleppe R, Molineux I, Khorana H (1971) Studies on polynucleotides. 96. Repair replication of short synthetic DNAs as catalyzed by DNA polymerases. J Mol Biol 56:341
3. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467.
4. Fischer S, Lumelsky N, Lerman L (1983) Separation of DNA fragments differing by single base substitution-application to beta-degrees-thalassemia identification. DNA - J Molec Cell Bio, 2:171
5. Fischer SG, Lerman LS (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: Correspondence with melting theory. Proc Natl Acad Sci USA 80:1579-1583
6. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350-1354
7. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51, Part 1:263-273
8. Kwok S, Mack DH, Mullis KB, Poiesz B, Ehrlich G., Blair D, Friedman-Kien A, Sninsky JJ (1987) Identification of human immunodeficiency virus sequences by using in vitro enzymatic amplification and oligomer cleavage detection. J Virol, 61:1690-1694
9. Bjørheim J, Gaudernack, G, Ekstrøm PO (2002) Melting gel techniques in single nucleotide polymorphism and mutation detection: From theory to automation. J Separation Science, 25:637-647
10. Bjørheim J, Ekstrøm PO (2005) Review of denaturant capillary electrophoresis in DNA variation analysis. Electrophoresis 26:2520-2530
11. Poland D (1974) Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations. Biopolymers 13:1859-1871
12. Myers RM, Fischer SG, Lerman LS, Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 13:3131-3145
13. Myers RM, Fischer SG, Maniatis T, Lerman LS (1985) Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. Nucleic Acids Res 13:3111-3129
14. Sheffield VC, Cox DR, Lerman LS, Myers RM (1989) Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci USA 86:232-236
15. Khrapko K, Hanekamp, JS, Thilly WG, Belenkii A, Foret F, Karger BL (1994) Constant denaturant capillary electrophoresis (CDCE): A high resolution approach to mutational analysis. Nucleic Acids Res 22:364-369
16. Kumar R, Hanekamp JS, Louhelainen J, Burvall K, Onfelt A, Hemminki K, Thilly WG (1995) Separation of transforming amino acid-substituting mutations in codons 12, 13 and 61 the N-ras gene by constant denaturant capillary electrophoresis (CDCE). Carcinogenesis 16:2667-2673
17. Bjørheim J, Lystad S, Lindblom A, Kressner U, Westring S, Wahlberg S, Lindmark G, Gaudernack G, Ekstrøm PO, Roe J et al. (1998) Mutation analyses of KRAS exon 1 comparing three different techniques: Temporal temperature gradient electrophoresis, constant denaturant capillary electrophoresis and allele specific polymerase chain reaction. Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 403:103-112
18. Ekstrøm PO, Børresen-Dayle AL, Qvist H, Giercksky KE, Thilly WG (1999) Detection of low-frequency mutations in exon 8 of the TP53 gene by constant denaturant capillary electrophoresis (CDCE). Biotechniques 27-12
19. Ekstrøm PO, Wasserkort R, Minarik M, Foret F, Thilly WG (2000) Two-point fluorescence detection and automated fraction collection applied to constant denaturant capillary electrophoresis. Biotechniques 29:582
20. Li-Sucholeiki XC, Khrapko K, Andre PC, Marcelino LA, Karger BL, Thilly WG (1999) Applications of constant dénaturant capillary electrophoresis/high-fidelity polymerase chain reaction to human genetic analysis. Electrophoresis 20:1224-1232
21. Li-Sucholeik, XC, Thilly WG (2000) A sensitive scanning technology for low frequency nuclear point mutations in human genomic DNA. Nucleic Acids Res 28:e44
22. Bjørheim J, Ekstrøm PO, Fossberg E, Børresen-Dale AL, Gaudernack G (2001) Automated constant dénaturant capillary electrophoresis applied for detection of KRAS exon 1 mutations. Biotechniques 30:972-975
23. Minarik M, Bjørheim, J, Ekstrøm PO, Dains KM (2001) High-throughput mutation detection and screening using MegaBACE (TM) capillary array instrument for genetic analysis. Amer J Human Genetics 69:469-469
24. Bjørheim J, Gaudernack G, Ekstrøm PO (2001) Mutation analysis of TP53 exons 5-8 by automated constant denaturant capillary electrophoresis. Tumor Biology 22:323-327
25. Kristense, AT, Bjorheim J, Minarik M, Giercksky KE, Ekstrom PO (2002) Detection of mutations in exon 8 of TP53 by temperature gradient 96-capillary array electrophoresis. Biotechniques 33:650-653
26. Bjørheim J, Minarik M, Gaudernack G, Ekstrøm PO (2002) Mutation detection in KRAS exon 1 by constant dénaturant capillary electrophoresis in 96 parallel capillaries. Analytical Biochemistry 304:200-205
27. Ekstrøm PO, Bjørheim J, Gaudernack G, Giercksky KE (2002) Population screening of single-nucleotide polymorphisms exemplified by analysis of 8000 alleles. J Biomolecular Screening 7:501-506
28. Bjørheim J, Abrahamsen TW, Kristensen AT, Gaudernack G, Ekstrøm PO (2003) Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis. Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis 526:75-83
29. Minarik M, Minarikova L, Bjorheim J, Ekstrom PO (2003) Cycling gradient capillary electrophoresis: A low-cost tool for high-throughput analysis of genetic variations. Electrophoresis 24:1716-1722
30. Kristensen AT, Bjorheim J, Wiig J, Giercksky KE, Ekstrom PO (2004) DNA variants in the ATM gene are not associated with sporadic rectal cancer in a Norwegian population-based study. Int J Colorectal Dise, 19:49-54
31. Hinselwood DC, Abrahamsen TW, Ekstrøm PO (2005) BRAF mutation detection and identification by cycling temperature capillary electrophoresis. Electrophoresis 26:2553-2561
32. Hinselwood DC, Warren DJ, Ekstrøm PO (2005) High-throughput gender determination using automated dénaturant gel capillary electrophoresis. Electrophoresis 26:2562-2566
33. Lorentzen AR, Celius EG, Ekstrøm PO, Wiencke K, Lie BA, Myhr KM, Ling V, Thorsby E, Vartdal F, Spurkland A et al (2005) Lack of association with the CD28/CTLA4/ICOS gene region among Norwegian multiple sclerosis patients. J Neuroimmunol, 166:197-201
34. Lind H, Zienolddiny S., Ekstrøm PO, Skaug V, Haugen A (2006) Association of a functional polymorphism in the promoter of the MDM2 gene with risk of nonsmall cell lung cancer. Int J Cancer 119:718-721
35. Harbo HF, Ekstrøm PO, Lorentzen AR, Sundvold-Gjerstad V, Celius EG, Sawcer S, Spurkland A (2006) Coding region polymorphisms in T cell signal transduction genes. Prevalence and association to development of multiple sclerosis. J Neuroimmunol 177:40-45
36. Bjørheim J, Minarik M, Gaudernack G, Ekstrøm PO (2003) Evaluation of denaturing conditions in analysis of DNA variants applied to multi-capillary electrophoresis instruments. J Separation Science, 26:1163-1168
37. Bracho MA, Moya A, Barrio E (1998) Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 79, Part 12:2921-2928
38. Li-Sucholeik, XC, Tomita-Mitchell A, Arnold K, Glassner BJ, Thompson T, Murthy JV, Berk L, Lange C, Leong-Morgenthaler, PM, MacDougall D et al (2005) Detection and frequency estimation of rare variants in pools of genomic DNA from large populations using mutational spectrometry. Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis 570:267-280
39. Li Q, Deka C, Glassner B, Arnold K, Li-Sucholeiki X, Tomita-Mitchell A, Thilly W, Karger B (2005) Design of an automated multicapillary instrument with fraction collection for DNA mutation discovery by constant denaturant capillary electrophoresis (CDCE). J Separation Science 28:1375-1389
40. Bjørheim J, Gaudernack G, Giercksky KE, Ekstrøm PO (2003) Direct identification of all oncogenic mutants in KRAS exon 1 by cycling temperature capillary electrophoresis. Electrophoresis 24:63-69
41. Fodde R, Losekoot M (1994) Mutation detection by denaturing gradient gel electrophoresis (DGGE). Hum Mutat 3:83-94
42. Ekstrøm PO, Bjørheim J (2006) Evaluation of sieving matrices used to separate alleles by cycling temperature capillary electrophoresis. Electrophoresis 27:1878-1885