From owner-biophysics@net.bio.net Thu Sep 10 23:00:00 1998
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From: paraleepk@aol.com (Paralee PK)
Newsgroups: bionet.biophysics
Subject: Re: 3-D structure of DNA
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Date: 11 Sep 1998 00:37:38 GMT
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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?



Paralee


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