DNA Structure and Replication

ID #2222

Could someone please explain melting temperature once more. Is it correct to say that if a DNA helix had even numbers of GC and AT bonds, at the melting temperature, more AT bonds would be halfway unwound compared to the GC bonds?

The Tm, or melting temperature, of a DNA helix is the temperature at which 50% of the double-stranded DNA helix are base paired by hydrogen bonding. You should think of the melting temperature as a measure of how much energy you have to add to get half of the DNA helix to become single stranded DNA. 

If you are comparing two DNA helices and one DNA helix has more A-T base pairs between the two strands and the other DNA helix has more G-C base pairs between the two strands, you would expect the A-T based paired helix to have a lower melting temperature than the G-C base paired helix. This is because A-T base pairs have two hydrogen bonds and G-C base pairs have three. So it takes less energy (in the form of heat) to break an A-T rich helix than it would to break a G-C rich helix, meaning the A-T helix has a lower melting temperature than the G-C rich helix. 

After that explanation, I hope it's clear that we're not talking about one base pair being halfway unwound as your question suggests. Two bases are either paired (creating dsDNA) or they are not (creating ssDNA). But you are on the right track that an A-T base pair in a helix that is at the melting temperature is more likely to be unpaired than a G-C base pair in the same helix. 

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