hit counter joomla

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?

tags: , , ,


(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.

New comments have been temporarily disabled. Please check back soon.