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I was looking up the fluorescent stain DAPI and seeing that it

binds strongly to A-T rich regions in DNA.

That made me wonder what is special about AT-rich regions.

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  • $\begingroup$ In bacteria AT-rich regions are usually binding sites for initiation of replication proteins. $\endgroup$ – user26720 Oct 28 '16 at 12:11
  • $\begingroup$ I edited your title as "traditional" didn't make sense. Not clear what you actually meant, but I think question works ok without it. $\endgroup$ – David Oct 28 '16 at 15:46
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With regards to DAPI itself, one could tell that the molecule itself has a shape complementary to the shape of A-T rich DNA. So in this case it's "special" because DAPI happens to have the structure to form bonds to A-T rich DNA regions. (There can very well be another organic molecule that binds to C-G rich regions). A quick google search will show how it looks like

dapi binding to dna

With regards to A-T in general, A-T share 2 hydrogen-bonds. However, this is not the reason why it's easier to break A-T rich regions. A-T rich regions destabilize the DNA double-helix. Refer to this http://nar.oxfordjournals.org/content/34/2/564.long. Transcription initiation occurs near T-A rich regions, e.g. TATA box in eukaryotes and Pribnow box in prokaryotes.

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