Correct Heteroduplex Formation for Mutation Detection Analysis

Overview

Journal Mol Diagn

Specialties Molecular Biology
Pathology

Date 2000 Jun 3

PMID 10837092

Authors

M J Smith

K E Humphrey

R Cappai

K Beyreuther

C L Masters

R G Cotton

Affiliations

Soon will be listed here.

Abstract

Background: The majority of mutation detection methods for unknown mutations are polymerase chain reaction (PCR)-based methods dependent on the formation of heteroduplexes between wild-type and mutant strands of DNA.

Methods And Results: This report discusses the difficulties associated with forming heteroduplexes with a large DNA fragment and the implications for subsequent mutation detection by the chemical cleavage of mismatch technique and other methods reliant on heteroduplex formation. It was found that the size and sequence context of the fragment being investigated inhibited correct heteroduplex formation. The problem was overcome by dividing the sequence into two overlapping fragments.

Conclusions: Early identification of this problem in other fragments will help with the rapid optimization of PCR-based mutation detection methods.

References

. The structure of the presenilin 1 (S182) gene and identification of six novel mutations in early onset AD families. Nat Genet. 1995; 11(2):219-22. DOI: 10.1038/ng1095-219. View

Danenberg P, Horikoshi T, Volkenandt M, Danenberg K, Lenz H, Shea L . Detection of point mutations in human DNA by analysis of RNA conformation polymorphism(s). Nucleic Acids Res. 1992; 20(3):573-9. PMC: 310425. DOI: 10.1093/nar/20.3.573. View

Hansen L, Justesen J, Kruse T . Sensitive and fast mutation detection by solid phase chemical cleavage. Hum Mutat. 1996; 7(3):256-63. DOI: 10.1002/(SICI)1098-1004(1996)7:3<256::AID-HUMU10>3.0.CO;2-1. View

Abrams E, Murdaugh S, LERMAN L . Comprehensive detection of single base changes in human genomic DNA using denaturing gradient gel electrophoresis and a GC clamp. Genomics. 1990; 7(4):463-75. DOI: 10.1016/0888-7543(90)90188-z. View

Verpy E, Biasotto M, Brai M, Misiano G, Meo T, Tosi M . Exhaustive mutation scanning by fluorescence-assisted mismatch analysis discloses new genotype-phenotype correlations in angiodema. Am J Hum Genet. 1996; 59(2):308-19. PMC: 1914725. View

Rowley G, Saad S, Giannelli F, Green P . Ultrarapid mutation detection by multiplex, solid-phase chemical cleavage. Genomics. 1995; 30(3):574-82. DOI: 10.1006/geno.1995.1279. View

Myers R, Fischer S, Maniatis T, LERMAN L . 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. 1985; 13(9):3111-29. PMC: 341224. DOI: 10.1093/nar/13.9.3111. View

Anwar R, Moynihan T, Ardley H, Brindle N, Coletta P, Cairns N . Molecular analysis of the presenilin 1 (S182) gene in "sporadic" cases of Alzheimer's disease: identification and characterisation of unusual splice variants. J Neurochem. 1996; 66(4):1774-7. DOI: 10.1046/j.1471-4159.1996.66041774.x. View

Crook R, Verkkoniemi A, Perez-Tur J, Mehta N, Baker M, Houlden H . A variant of Alzheimer's disease with spastic paraparesis and unusual plaques due to deletion of exon 9 of presenilin 1. Nat Med. 1998; 4(4):452-5. DOI: 10.1038/nm0498-452. View

10.

Kuklin A, Munson K, Gjerde D, Haefele R, Taylor P . Detection of single-nucleotide polymorphisms with the WAVE DNA fragment analysis system. Genet Test. 1997; 1(3):201-6. DOI: 10.1089/gte.1997.1.201. View

11.

Cotton R, Rodrigues N, Campbell R . Reactivity of cytosine and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. Proc Natl Acad Sci U S A. 1988; 85(12):4397-401. PMC: 280436. DOI: 10.1073/pnas.85.12.4397. View

12.

Cole W, Chiodo A, Lamande S, Janeczko R, Ramirez F, Dahl H . A base substitution at a splice site in the COL3A1 gene causes exon skipping and generates abnormal type III procollagen in a patient with Ehlers-Danlos syndrome type IV. J Biol Chem. 1990; 265(28):17070-7. View

13.

Youil R, Kemper B, Cotton R . Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc Natl Acad Sci U S A. 1995; 92(1):87-91. PMC: 42822. DOI: 10.1073/pnas.92.1.87. View

14.

Orita M, Suzuki Y, Sekiya T, Hayashi K . Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics. 1989; 5(4):874-9. DOI: 10.1016/0888-7543(89)90129-8. View

15.

Verpy E, Biasotto M, Meo T, Tosi M . Efficient detection of point mutations on color-coded strands of target DNA. Proc Natl Acad Sci U S A. 1994; 91(5):1873-7. PMC: 43266. DOI: 10.1073/pnas.91.5.1873. View

16.

Perez-Tur J, Froelich S, Prihar G, Crook R, Baker M, Duff K . A mutation in Alzheimer's disease destroying a splice acceptor site in the presenilin-1 gene. Neuroreport. 1995; 7(1):297-301. View

17.

Ganguly T, Dhulipala R, Godmilow L, Ganguly A . High throughput fluorescence-based conformation-sensitive gel electrophoresis (F-CSGE) identifies six unique BRCA2 mutations and an overall low incidence of BRCA2 mutations in high-risk BRCA1-negative breast cancer families. Hum Genet. 1998; 102(5):549-56. DOI: 10.1007/s004390050738. View

18.

Gibbs R, Caskey C . Identification and localization of mutations at the Lesch-Nyhan locus by ribonuclease A cleavage. Science. 1987; 236(4799):303-5. DOI: 10.1126/science.3563511. View

19.

Freeman G, Huang A . Mapping temperature-sensitive mutants of vesicular stomatitis virus by RNA heteroduplex formation. J Gen Virol. 1981; 57(Pt 1):103-17. DOI: 10.1099/0022-1317-57-1-103. View

20.

White M, Carvalho M, Derse D, OBrien S, Dean M . Detecting single base substitutions as heteroduplex polymorphisms. Genomics. 1992; 12(2):301-6. DOI: 10.1016/0888-7543(92)90377-5. View