Chemical cleavage of mismatch: A new look at an established method1

Human Mutation

Volumn 11, Issue 5, 1998, Pages 345-353

  Ellis, Timothy P ^a   Humphrey, Karen E ^a   Smith, Margaret J ^a,b   Cotton, Richard G H ^a  

^a ST VINCENT S HOSPITAL   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Chemical cleavage; Fluorescent analysis; Mutation detection

Indexed keywords

DNA FRAGMENT; HETERODUPLEX; HYDROXYLAMINE; OSMIUM TETRAOXIDE;

BASE MISPAIRING; CHEMICAL ANALYSIS; CLINICAL PROTOCOL; DNA CLEAVAGE; DNA SEQUENCE; FLUORESCENCE; HUMAN; METHODOLOGY; MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW;

EID: 0031965814     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1098-1004(1998)11:5<345::AID-HUMU1>3.0.CO;2-0     Document Type: Review

References (68)

1. Akli S, Chomet JC, Lacorte JM, Bachner L, Poenaru A, Peonaru L (1993) Ten novel mutations in the HEXA gene in non-Jewish Tays-Sachs patients. Hum Mol Genet 2:61-67.
2. Anderson MJ, Milner CM, Cotton RGH, Campbell RD (1992) The coding sequence of the hemolytically inactive C4A6 allotype of human complement component C4 reveals that a single arginine to tryptophan substitution at β-chain residue 458 is the likely cause of the defect. J Immun 148:2795-2802.
3. Basler E, Grompe U, Parenti G, Yates J, Ballabio A (1992) Identification of point mutations in the steroid sulfatase gene of three patients with X-linked ichthyosis. Am J Hum Genet 50:483-491.
4. Bateman JF, Lamande SR, Hannagan M, Müller I, Dahl H-HM, Cole WG (1993) Chemical cleavage method for the detection of RNA base changes. Experience in the application to collagen mutations in osteogenesis imperfecta. Am J Med Genet 45:233-240.
5. Biasotto M, Meo T, Tosi M, Verpy E (1996) FAMA: Fluorescence-assisted mismatch analysis by chemical cleavage In Landegren U (ed): Laboratory Protocols for Mutation Detection Oxford: Oxford University Press, pp 54-60
6. Bugg BY, Danks MK, Beck WT, Suttle DP (1991) Expression of a mutant DNA topoisomerase II in CCRF-CEM human leukaemic cells selected for resistance to teniposide. Proc Natl Acad Sci USA 88:7654-7658.
7. Cecchi C, Biasotto M, Tosi M, Avner P (1997) The mottled mouse as a model tor human Menkes disease: Identification of mutations in the Atp7a gene. Hum Mol Genet 6:425-433.
8. Condie A, Eeles R, Borresen A-L, Coles C, Cooper C, Prosser J (1993) Detection of point mutations in the p53 gene. Comparison of single-strand conformation polymorphism, constant denaturant gel electrophoresis, and hydroxylamine and osmium tetroxide techniques. Hum Mutat 2:58-66.
9. Cotton RGH (1993) Current methods of mutation detection. Mut Res 285:125-144.
10. Cotton RGH (1997) Mutation Detection. Oxford: Oxford University Press.
11. Cotton RGH, Campbell RD (1989) Chemical reactivity of matched cytosine and thymine bases near mismatched and unmatched bases m a heteroduplex between DNA strands with multiple differences. Nucl Acids Res 17:4223-4233.
12. Cotton RGH, Wright PJ (1989) Rapid chemical mapping of dengue virus variability using RNA isolated directly from cells. J Virol Methods 26:67-76.
13. Cotton RGH, Grompe M (1994) Chemical cleavage of heteroduplex DNA to identify mutations. In Dracopoli NC, Haines JL, Korf BR, Moir DT, Morton CC, Seidman CE, Seidman JA, Smith DR (ed): Current Protocols in Human Genetics. Greene/Wiley, pp 7.6.1-7.6.9.
14. Cotton RGH, Rodrigues NR, Campbell RD (1988) Reactivity of cytosme and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. Proc Natl Acad Sci USA 85:4397-4401.
15. Cotton RGH, Dahl H-HM, Forrest SM, Howells DW, Ramus SJ, Bishop RE, Dianzani I, Saleeba JA, Palombo E, Anderson MJ, Milner CM, Campbell RD (1993) Analysis of sequence contexts flanking T-G mismatches leads to predictions about reactivity of the mismatched T to osmium terroxide. DNA and Cell Biology 12:945-949.
16. Curiel DT, Buchhagen DL, Chiba I, D'Amico D, Takahashi T, Minna JD (1990) A chemical mismatch cleavage method useful for the detection of point mutations in the p53 gene in lung cancer. Am J Respir Cell Mol Biol 3:405-411.
17. Dahl H-HM, Lamande SR, Cotton RGH, Bateman JF (1989) Detection and localization of base changes in RNA using a chemical cleavage method. Anal Biochem 183:263-268.
18. Dahl H-HM, Lamande SR, Cotton RGH, Cole WG, Bateman JF (1990a) A rapid chemical cleavage method for the detection and localization of base changes in RNA and DNA. UCLA Symposia on Molecular and Cellular Biology, Biotechnology and Human Genetic Predisposition to Disease. Proceedings 126:209-218.
19. Dahl H-HM, Maragos C, Brown RM, Hansen LL, Brown GK (1990b) Pyruvate dehydrogenase deficiency caused by deletion of a 7-bp repeat sequence in the E1α gene. Am J Hum Genet 47:286-293.
20. Das S, Levinson B, Whitney S, Vulpe C, Packman S, Gitschier J (1994) Diverse mutations in patients with Menkes disease often lead to exon skipping. Am J Hum Genet 55:883-889.
21. Dawson SJ, Wiman B, Hamsten A, Green F, Humphries S, Henney A (1993) The two allele sequences of a common polymorphism in the promoter of the plasminogen activator inhibitor-1 (PAI-1) gene respond differently to interleukin-1 in HepG2 cells. J Biol Chem 268:10739-10745.
22. Dianzani I, Camaschella C, Saglio G, Forrest SM, Ramus S, Cotton RGH (1991a) Simultaneous screening for beta-thalassemia mutations by chemical cleavage of mismatch. Genomics 11:48-53.
23. Dianzani I, Forrest SM, Camaschella C, Gottardi E, Cotton RGH (1991b) Heterozygotes and homozygotes: Discrimination by chemical cleavage of mismatch. Am J Hum Genet 48:423-424.
24. Dianzani I, Howells DW, Ponzone A, Saleeba JA, Smooker PM, Cotton RGH (1993) Two new mutations in the dihydropteridine reductase gene in patients with tetrahydrobiopterin deficiency. J Med Genet 30:465-469.
25. Dry KL, Alfred MA, Edgar AJ, Brown J, Manson FD, Ho MF, Prosser J, Hardwick LJ, Lennon AA, Thomson K (1995) Identification of a novel gene, ETX1 from Xp21.1, a candidate gene for X-linked retintis pigmentosa (RP3). Hum Mol Genet 4:2347-2353.
26. Forrest SM, Dahl HH, Howells DW, Dianzani I, Cotton RGH (1991) Mutation detection in phenylketonuria by using chemical cleavage of mismatch: Importance of using probes from both normal and patient samples. Am J Hum Genet 49:175-183.
27. Germain D, Biasotto M, Tosi M, Meo T, Kahn A, Poenaru L (1996) Fluorescence-assisted mismatch analysis (FAMA) for exhaustive screening of the α-galactosidase A gene and detection of carriers in Fabry disease. Hum Genet 98:719-726.
28. Green PM, Rowley G, Saad S, Gianelli F (1996) Multiplex solid phase fluorescent chemical cleavage. In Landegren U (ed): Laboratory Protocols for Mutation Detection. Oxford. Oxford University Press, pp 61-64.
29. Grompe M, Caskey CT, Fenwick RG (1991a) Improved molecular diagnostics for ornithine transcarbamylase deficiency. Am J Hum Genet 48:212-222.
30. Grompe M, Versalovic J, Koeuth T, Lupski JR (1991b) Mutations in the Escherichia coli dnaG gene suggest coupling between DNA replication and chromosome partitioning. J Bacteriol 173:1268-1278.
31. Grompe M, Al-Dhalimy M (1993) Mutations of the fumarylacetoacetate hydrolase gene in four patients with tyrosinemia, type I. Hum Mutat 2:85-93.
32. Han M, Sternberg PW (1990) let-60, a gene that specifies cell fates during C. elegans vulval induction, encodes a ras protein. Cell 63:921-931
33. Hansen LL, Justesen J, Kruse TA (1996) Sensitive and fast mutation detection by solid phase chemical cleavage. Hum Mutat 7:256-263.
34. Haris II, Green PM, Bentley DR, Giannelli F (1994) Mutation detection by fluorescent chemical cleavage. Application to hemophilia B. PCR Methods Appl 3 268-271.
35. Kilimann MW, Pizzuti A, Grompe M, Caskev CT (1992) Point mutations and polymorphisms in the human dystrophin gene identified in genomic DNA sequences amplified by multiplex PCR. Hum Genet 89:253-258.
36. Liddell MB, Bayer AJ, Owen MJ (1995) No evidence that common allelic variation in the Amyloid Precursor Protein (APP) gene confers susceptibility to Alzheimer's disease. Hum Mol Genet 4:853-858.
37. Lin B, Cotton RGH, Trent DW, Wright PJ (1992) Geographical clusters of dengue virus type 2 isolates based on analysis of infected cell RNA by the chemical cleavage at mismatch method. J Virol Methods 40:205-218
38. Little MH, Prosser J, Condie A, Smith PJ, Van Heyningen V, Hastie ND (1992) Zinc finger point mutations within the WT1 gene in Wilms tumour patients. Proc Natl Acad Sci USA 89:4791-4795.
39. Mashal RD, Koontz J, Sklar J (1995) Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nature Genet 9:177-183.
40. Montandon AJ, Green PM, Bentley DR, Ljung R, Kling S, Nilsson IM, Giannelli F (1992) Direct estimate of the haemophilia B (factor IX deficiency) mutation rate and of the ratio of the sex-specific mutation rates in Sweden. Hum Genet 89:319-322.
41. Mottes M, Sangalli A, Valli M, Forlino A, Gomez-Lira M, Antoniazzi F, Constantinou-Deltas CD, Cetta G, Pignatti PF (1994) A base substitution at IVS-19 3′-end splice junction causes exon 20 skipping in proα2(I) collagen mRNA and produces mild osteogenesis imperfecta. Hum Genet 93:681-687.
42. Nakamura M, Nakano S, Goto Y, Ozawa M, Nagahama Y, Fukuyama H, Akiguchi I, Kaji R, Kimura J (1995) A novel point mutation in the mirochondrial tRNA (Ser(UCN)) gene detected in a family with MERFF/MELAS overlap syndrome. Biochem Biophys Res Commun 214:86-93.
43. Palombo EA, Bishop RF, Cotton RGH (1993a) Sequence conservation within neutralization epitope regions of VP7 and VP4 proteins of human serotype G4 rotavirus isolates. Arch Virol 133:323-334.
44. Palombo EA, Bishop RF, Cotton RGH (1993b) Intra- and inter-season genetic variability in the VP7 gene of serotype 1 (monotype 1a) rotavirus clinical isolates. Arch Virol 130:57-69.
45. Prosser J (1997) Chemical cleavage of mismatch in heteroduplexes. In Taylor GR (ed): Laboratory Methods for the Detection of Mutations and Polymorphisms in DNA. Boca Raton: CRC Press, pp 225-235.
46. Prosser J, Condie A, Wright M, Horn JM, Fantes JA, Wyllie AH, Dunlop MG (1994) APC mutation analysis by chemical cleavage of mismatch and a protein truncation assay in familial adenomatous polyposis. Br J Cancer 70:841-846.
47. Purandare SM, Lanyon WG, Connor JM (1994) Characterisation of inherited and sporadic mutations in neurofibromatosis type-1. Hum Mol Genet 3:1109-1115.
48. Ramus SJ, Cotton RGH (1995) Mutations Ivs4nt1, 47delCT, and G148S identified in the phenylalanine hydroxylase gene by RT-PCR of illegitimate transcripts and chemical cleavage of mismatch. Hum Mutat 6:250-251.
49. Ramus SJ, Cotton RGH (1996a) Single-tube chemical cleavage of mismatch: Successive treatment with hydroxylamine and osmium tetroxide. Biotechniques 21:216-220.
50. Ramus SJ, Cotton RGH (1996b) Chemical cleavage of mismatch In Landegren U (ed): Laboratory Protocols for Mutation Detection. Oxford: Oxford University Press, pp 61-64.
51. Rodrigues NR, Rowan A, Smith MEF, Kerr IB, Bodmer WF, Gannon JV, Lane DP (1990) p53 mutations in colorectal cancer. Proc Natl Acad Sci USA 87:7555-7559.
52. Rowley G, Saad S, Giannelli F, Green PM (1995) Ultrarapid mutation detection by multiplex, solid-phase chemical cleavage. Genomics 30:574-582.
53. Rudzki Z, Duncan EM, Casey GJ, Neumann M, Favaloro EJ, Lloyd JV (1996) Mutations in a subgroup of patients with mild haemophilia A and a familial discrepancy between the one-stage and two-stage factor VIII.C methods. Br J Haem 94:400-406.
54. Saito H, Grompe M, Neeley TL, Jakobs PM, Moses RE (1994) Fanconi anemia cells have a normal gene structure for topoisomerase I. Hum Genet 93:583-586.
55. Saleeba JA, Ramus SJ, Cotton RGH (1992) Complete mutation detection using unlabeled chemical cleavage. Hum Mut 1:63-69.
56. Sheridan E, Hancock BW, Goyns MH (1993) High incidence of mutations of the p53 gene detected in ovarian tumours by the use of chemical mismatch cleavage Cancer Letters 68:83-89.
57. Smooker PM and Cotton RGH (1993) The use of chemical reagents in the detection of DNA mutations. Mut Res 288:65-77.
58. Theophilus BDM, Latham T, Grabowski GA, Smith FI (1989) Comparison of RNase A, chemical cleavage and GC-clamped denaturing gradient gel electrophoresis for the detection of mutations in exon 9 of the human acid β-glucosidase gene. Nucleic Acids Res 17:7707-7722.
59. Tosi M, Verpy E, Meo T (1997) Detection of mutations by fluorescence-assisted mismatch analysis. (FAMA). In Dracopoli NC, Haines JL, Korf BR, Moir DT, Morton CC, Seidman CE, Seidman JG, Smith DR (ed): Current Protocols in Human Genetics. Greene/Wiley pp 7.8.1-7.8.11.
60. Tsuboi K, Nose T, Okinaka RT, Chen DJ (1995) Non-radioactive mismatch analysis to detect small mutations in human hypoxanthine-guanine phosphoribosyl transferase cDNA. Jpn J Med Sci Biol 48:163-175.
61. Tümmler B, Dük T, Kubesch P, Fislage R, Kälin N, Neumann T, Wulbrand U, Wulf B, Steinkamp G, von der Hardt H (1993) Cystic fibrosis: The impact of analytical technology for genotype-phenotype studies. Clin Chim Acta 217:23-28.
62. Veitia R, Ion A, Barbaux S, Jobling MA, Souleyreau N, Ennis K, Ostrer H, Tosi M, Chibani J, Fellous M, McElreavey K (1997) Mutations and sequence variants in the testis-determining region of the Y chromosome in individuals with a 46,XY female genotype. Hum Genet 99:648-652.
63. Verpy E, Biasotto M, Meo T, Tosi M (1994) Efficient detection of point mutations on color-coded strands of target DNA. Proc Natl Acad Sci USA 91:1873-1877.
64. Verpy E, Biasotto M, Brai M, Misiano G, Meo T, Tosi M (1996) Exhaustive mutation scanning by fluorescence-assisted mismatch analysis discloses new genotype-phenotype correlations in angioedema. Am J Hum Genet 59:308-319.
65. Wright PJ and Cotton RGH (1990) Characterization of sequence variation among isolates of RNA viruses: Detection of mismatched cytosine and thymine in RNA-DNA heteroduplexes by chemical cleavage. In Brinton MA, Heinz FX (eds): New Aspects of Positive-Strand RNA Viruses. Washington: American Society for Microbiology, pp 41-44.
66. Xu CF, Talmud P, Schuster H, Houlston R, Miller G, Humphries S (1994) Association between genetic variation at the APO AICIII-AIV gene cluster and familial combined hyperlipidaemia Clin Genet 46:385-397.
67. Youil R, Kemper B, Cotton RGH (1995) Screening for mutations by enzyme cleavage using T4 endonuclease VII. Proc Natl Acad Sci USA 92:87-91.
68. Zerwekh JE, Hughes MR, Reed BY, Breslau NA, Heller HJ, Lemke M, Nasonkin I, Pak CYC (1995) Evidence for normal vitamin D receptor messenger ribonucleic acid and genotype m absorptive hypercalciuria. J Clin Endocrinol Metab 80:2960-2965.