Microsoft (R) Word (TM) Macro for analysis of cytosine methylation by the bisulfite deamination reaction

Cytosine methylation at CpG dinucleotides is an important control mechanism in development differentiation, and neoplasia. Bisulfite genomic sequencin g and its modifications have been developed to examine methylation at these CpG dinucleotides. To use these methods, one has to (i) manually convert t he sequence to that produced by bisulfite conversion and PCR amplification, taking into account that cytosine residues at CpG dinucleotides may or may not be converted depending on their methylation status. (ii) identify rele vant restriction sites that may be used for methylation analysis, and (iii) conduct similar steps with the other DNA strand since the two strands of D NA are no longer complementary after bisulfite conversion. To automate thes e steps, we have developed a macro that can be used,with Microsoft(R) Word( TM). This macro (i) converts genomic sequence to modified sequence that wou ld result after bisulfite treatment facilitating primer design for bisulfit e genomic sequencing and methylation-sensitive PCR assay and (ii) identifie s restriction sites that are preserved in bisulfite-converted and PCR-ampli fied product only if cytosine residues at relevant CpG dinucleotides are me thylated (and thereby not converted to uracil) in the genomic DNA.