Okay, all of you biochemists and molecular biology types. I have a puzzle for you that I found by accident during a lecture. Yes, I was the one lecturing and the notes will be posted soon.
In the meantime, here’s your puzzle: What’s unusual about this pair of bases?
tags: DNA structure, DNA , molecular structure, biochemistry
(Those of you who attended our Chautauqua course – I know you probably know the answer – but don’t answer, okay?)
Looks like the strands are parallel rather than the normal antiparallel, and the hydrogen bonding between A & T is non-standard. Normally, the amine of A would bond with O4 of T. Instead, it’s bonded with O2. (There’s probably a name for this non-standard H-bonding scheme, but I don’t remember what it is.)
[BTW, to be pedantic, the picture actually shows a pair of nucleotides.]
Do I win? 
Qetzal:
You can be as pedantic as you like, but these two nucleotides do form a basepair because they are held together by hydrogen bonds.
It does look like there are only two nucleotides because I hid the other 11 basepairs in order to emphasize the weirdness of this structure. These nucleotides or this basepair are part of a double-stranded piece of DNA that’s 12 basepairs long.
As far as your guess and whether you’re right or not – I’ll post the answer on Friday.
qetzal is correct, the A is flipped relative to the T, which changes the H-bond arangement. This is neither Watson-Crick nor Hoogsteen pairing. As to whether the strands are parallel vs. anti-parallel, I’d have to see more of the context.
My old copy of Saenger’s Principles of Nucleic Acid Structure calls it a “reversed Watson Crick” base pair.
As for orientation, I guess it’s a little hard to say parallel ‘strands’ with only two nucleotides. But it does seem clear that both 5′ carbons are coming towards the viewer.
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July 10, 2007
July 10, 2007
July 11, 2007