Regarding Conversion - (Mar/16/2011 )

hi Greetings

we are working on Sex-specific expression of lipocalins in hamsters, we are planing to start investigating the methylation state of the gene and its promoter. but we afraid, that we may face some difficulties in doing that.

1. There are 2 genes 85% similar to each other and they differ in hardly few bases in different regions.
one may be methylated and another may not be methylated or both are unmethylated and regulated by some other means of gene regulation. in case if am designing primer not spanning any CpG then it will amplify both the similar genes and and sequencing data may be confusing to analyse. what we planing is after converting the DNA and PCR amplification, cloning of the PCR products and screening of the clones for our gene. Is there any method for studying methylation in multiple copy genes????????????

kindly suggest : should i maintain the DNA template quality very high, or some shearing can be allowd. how the quality of DNA affect bisulphite conversion.
and also suggest me protocol or kit to purify high quality DNA from tissue samples.???????
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I know some genes have many copies in the genome with almost identical mRNA sequence, however, their promoter sequences or 5'flanking sequences may differ significantly. Are you sure the promoter sequence for your gene has great homology with its copies?

You don't need extra high quality DNA, any DNA isolation kit should work.