Dear all, I'm studying DNA-Protein relationships for a computer simulation I have to make about it and I'm finding it difficult to understand how the RNA polymerase knows where to start and stop transcription on a strand of DNA. Could someone explain this for me? Let's assume that '[' indicates the start of a gene (start codon? tata-box? promoter?) and ']' indicates the end of a gene (stop codon? transcription terminator?). Are all '[' and ']' markers well-formed brackets? Can you have over lapping genes as in [..[..]..]? Can you have missing brackets as in [.. or ..]? If not, what happens if this is the case? Thanks a lot!