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Different denaturation rates between methylated and non-methylated genomic DNA can result in allele-specific PCR amplification

Different denaturation rates between methylated and non-methylated genomic DNA can result in allele-specific PCR amplification
Different denaturation rates between methylated and non-methylated genomic DNA can result in allele-specific PCR amplification
We analysed a DNA sample from a father and child who were both heterozygous for a 7 base pair insertion in the MEST gene differentially-methylated promoter region, previously shown by PCR analysis of bisulphite-treated DNA to be on the methylated allele in the unaffected father and the unmethylated allele in the affected child. PCR from genomic DNA was then carried out using a commercial PCR kit with its recommended initial DNA denaturation step of 2 minutes. Subsequent sequence analysis showed that only the non-methylated allele had been amplified, the father appearing to be homozygous normal and the child appearing to have a homozygous 7 b.p. insertion. The PCR protocol was then modified in order to use a longer DNA denaturation stage prior to the addition of the polymerase enzyme. Upon doing so, both the methylated and non-methylated alleles were then identifiable by sequencing with the mutation appearing in its expected heterozygous form. These results highlight the fact that the methylation status of DNA can affect the denaturation rate prior to PCR and result in allele drop-out, showing that the standard protocols of commercial kits should be used with caution when working with methylated regions of DNA.
differential methylation, allele-specific PCR, commercial kit
2162-4453
13-14
Bunyan, David J.
dd9134b9-f889-44cc-83cc-a41fc5d74d69
Bullman, Hilary M.S.
4a36eca8-a144-4360-b421-aba1ed7bfb70
Lever, Margaret
4d112693-a8b5-46d9-8759-29e3677f31d6
Saminathan, Sasi D.
a33890a1-abc8-44c0-abcc-07394ea6d2dd
Keng, Wee Teik
e13d7e9f-35c8-4aa1-bc72-116f534ec807
Araffin, Roziana
bdd5622d-5266-4968-b76f-b3989b6f4bf5
Robinson, David O.
9db1b26b-6c2b-4ac5-879e-20f8a2dc30ec
Bunyan, David J.
dd9134b9-f889-44cc-83cc-a41fc5d74d69
Bullman, Hilary M.S.
4a36eca8-a144-4360-b421-aba1ed7bfb70
Lever, Margaret
4d112693-a8b5-46d9-8759-29e3677f31d6
Saminathan, Sasi D.
a33890a1-abc8-44c0-abcc-07394ea6d2dd
Keng, Wee Teik
e13d7e9f-35c8-4aa1-bc72-116f534ec807
Araffin, Roziana
bdd5622d-5266-4968-b76f-b3989b6f4bf5
Robinson, David O.
9db1b26b-6c2b-4ac5-879e-20f8a2dc30ec

Bunyan, David J., Bullman, Hilary M.S., Lever, Margaret, Saminathan, Sasi D., Keng, Wee Teik, Araffin, Roziana and Robinson, David O. (2011) Different denaturation rates between methylated and non-methylated genomic DNA can result in allele-specific PCR amplification. Open Journal of Genetics, 2011/01 (2), 13-14. (doi:10.4236/ojgen.2011.12003).

Record type: Article

Abstract

We analysed a DNA sample from a father and child who were both heterozygous for a 7 base pair insertion in the MEST gene differentially-methylated promoter region, previously shown by PCR analysis of bisulphite-treated DNA to be on the methylated allele in the unaffected father and the unmethylated allele in the affected child. PCR from genomic DNA was then carried out using a commercial PCR kit with its recommended initial DNA denaturation step of 2 minutes. Subsequent sequence analysis showed that only the non-methylated allele had been amplified, the father appearing to be homozygous normal and the child appearing to have a homozygous 7 b.p. insertion. The PCR protocol was then modified in order to use a longer DNA denaturation stage prior to the addition of the polymerase enzyme. Upon doing so, both the methylated and non-methylated alleles were then identifiable by sequencing with the mutation appearing in its expected heterozygous form. These results highlight the fact that the methylation status of DNA can affect the denaturation rate prior to PCR and result in allele drop-out, showing that the standard protocols of commercial kits should be used with caution when working with methylated regions of DNA.

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More information

Published date: September 2011
Keywords: differential methylation, allele-specific PCR, commercial kit
Organisations: Human Development & Health

Identifiers

Local EPrints ID: 339246
URI: http://eprints.soton.ac.uk/id/eprint/339246
ISSN: 2162-4453
PURE UUID: 51458c5d-36d6-4f95-a321-698cdff68082

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Date deposited: 25 May 2012 09:56
Last modified: 14 Mar 2024 11:13

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Contributors

Author: David J. Bunyan
Author: Hilary M.S. Bullman
Author: Margaret Lever
Author: Sasi D. Saminathan
Author: Wee Teik Keng
Author: Roziana Araffin
Author: David O. Robinson

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