how to work out curvature of DNA???

Laurentiu COCEA cocea at citi2.fr
Wed Jul 5 11:47:12 EST 1995


gqva12 at udcf.gla.ac.uk (G Gallagher) wrote:
>
> Hello out there
> 
> Does anyone know how to work out the extent to which the secondary structure
> and/or curvature of dsDNA is altered by mutations?
> 
> Specifically, I want to guage the effect of differing sizes of a CA repeat.
> 
> There doesn't seem to be an obvious programme in the GCG package.
> 
> Many thanks
> 
> Grant Gallagher

Hi- if by "mutations" you mean nucleotide substitutions, then I don't 
think this can change the "secondary structure" of a dsDNA. Actually,
a secondary structure is either a hairpin structure of a dsDNA (does it
occur in vivo?) or a Z-DNA. Never heard of a "secondary structure" of 
a dsDNA and if you actually think of DNA bending then it depends on
specific proteins that are able to do it by specific interections with
the nucleotides. On the other hand, a dsDNA fgt of less than 250 bp
does not bend well, at least it cannot bend enough to have its ends
"touch" each other - so there are some limitations. 

One of the main features of a dsDNA molecule is the fact that 
its structure (the double helix) does NOT depend on the specific 
sequence of nucleotides that make it. On the other hand, protein
secondary structures do depend on their primary structure (i.e., 
the sequence of amino acids).

If you think different and you have some arguments please let me know. 

Laurentiu
  




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