Assessing alternative base substitutions at primer CpG sites to optimise unbiased PCR amplification of methylated sequences.

ABSTRACT:

Background

Determining the role of DNA methylation in various biological processes is dependent on the accurate representation of often highly complex patterns. Accurate representation is dependent on unbiased PCR amplification post bisulfite modification, regardless of methylation status of any given epiallele. This is highly dependent on primer design. Particular difficulties are raised by the analysis of CpG-rich regions, which are the usual regions of interest. Here, it is often difficult or impossible to avoid placing primers in CpG-free regions, particularly if one wants to target a specific part of a CpG-rich region. This can cause biased amplification of methylated sequences if the C is placed at those positions or to unmethylated sequences if a T is placed at those positio

SUBMITTER: Candiloro ILM 

PROVIDER: S-EPMC5379501 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature