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A DNA puzzle

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?

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(Those of you who attended our Chautauqua course – I know you probably know the answer – but don’t answer, okay?)


  1. #1 qetzal
    July 10, 2007

    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? :-)

  2. #2 Sandra Porter
    July 10, 2007


    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.

  3. #3 Tegumai Bopsulai, FCD
    July 11, 2007

    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.

  4. #4 qetzal
    July 11, 2007

    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.