3-D structure of DNA

Paralee PK paraleepk at aol.com
Thu Sep 10 19:39:41 EST 1998


I did kind of wonder about INADEQUATE.  Thanks for clearing that up.  Alot of
the methods you suggest are not in the general texts.  We have been referred to
Glasel's - Introduction to Biophysical Methods . . .  but it isn't available at
the moment (I'm bugging the prof to get it on reserve).

Thank you for your advice.  I did some reading today.  Your clues provided me
with some direction.  I think I'll have some hypotheses by tommorow as far as
the specific probable structures.  Right now I'm pretty sure it:
-isn't circular: need to have 80 bp minimum to circularize
-isn't Z-DNA in any portion: need alternatine purine pyrimidine and
supercoiling that can only occur in circular DNA
-could be 3x helical, but that requires supercoiling/circularization which I'm
assuming we don't have . . . the "breathing and fraying" of the A*T region
wouldn't provide enough energy to make this happen would it?
-could be bent 8.7 degrees for each dinucleotide, best seen if a long repeating
strip were synthesized
-could be slipping- my teacher said left slipping (because of backbone config.)
is preffered, does that mean the 5' end slips to the left/
-is not forming cruciform: supercoiling required for energy needed, hairpin has
to have 3-4 unpaired bases in it, 10 base pairs minimum are required

Do these conclusions seem right? I based them mostly on what I read in Sinden's
book-DNA Structure and Function.

I'm tending to think of using:
NMR-NOE
Tm-Absorbance

At first I wanted to use an enzymatic digest to select for single stranded DNA,
but I don't think there is going to be much.  I need to find out more about
NMR-NOE.  Glasel's book seems to be unavailable here.  Any other resources?

Thank you for your listening ear!

Paralee



More information about the Molmodel mailing list