Question about Base Pairs...

[Bill Nye Guy]

alright this may have a obvious answer, but i was woundering why is it that Adenine and Guanine or Cytosine and Thymine can not pair up. I know it deals with the molecular structure of the base pairs, but can someone explain indepth why their can't be a pair like Adenine and Guanine on a spot on the DNA.

 

Thanks alot everyone

[Bluenoise]

It because one pair makes 2 hydrogen bonds between them and the other makes 3. IE the number of hydrogen donors and exceptors must match.

 

they shows it

 

http://en.wikipedia.org/wiki/Image:Dna_pairing_aa.gif

[Yggdrasil]

Basically it's a problem of geometry. Only A-T and G-C basepairs fit inside the geometry of the B-DNA helix. Outside the context of double stranded DNA, you can have unconventional base pairs -- for example, you ocassionally find G-U basepairs in RNA.

[zyncod]

Outside the context of double stranded DNA, you can have unconventional base pairs

 

Actually, some secondary structures in repetitive regions probably have unconventional base pairs since the base stacking interactions are messed up (I've never actually seen a crystal structure of that, tho).

 

On a side note, Yggdrasil, I can't believe that you have the chair conformation for glucose as your icon/avatar/whatever. I cannot think of anything that I've ever hated more than organic chem.

[Bluenoise]

errrm nm

[mattbimbo]

what about mismatch repair? a beautiful system, first studied in ecoli, where it was also demonstrated how the repair of mismatches was determined by the parental strand in a newly replicated DNA molecule -

thereby preseverving DNA integrity.

 

a number of crystal structures of mismatch enzymes complexed with duplexes that contain mismatches. crystal structures of enzymes with DNA published very well 10-15 years ago.

[mattbimbo]

if you can access CELL papers,

a colleague in my lab remembered this recent paper with lambda protein and misaligned DNA:

http://www.cell.com/content/article/abstract?uid=PIIS0092867405013243

[Mercurial]

It's not so much that they can't pair up it's just 1) not energetically favorable b/c of H-bonding and 2) there is a lot of cell machinery that corrects these errors (most of the time) when they happen. if you take a look at the "wiggle position" in tRNA during translation (I've completely switched to RNA on ya real quick) These frequently don't perfectly base pair and sometimes even have different nucleic acids than the normal ACTGU in this 3rd position. That accounts for 4x4x4 = 64 different possible codons coding for only 20 (I think?) amino acids.