how to work out curvature of DNA???

Yasha Hartberg Yasha at bioch.tamu.edu
Wed Jul 5 08:17:44 EST 1995


In article <gqva12.804957756 at cent.gla.ac.uk>, 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.

Secondary structure prediction of DNA is not as well established as for
RNA, but you may be able to use the same algorithms as RNA secondary
structure prediction programs by substituting in the free energy values
determined recently for DNA base stacking.  As for DNA bending, I don't
think it is well enough understood to develop prediction algorithms. 
There are experimental techniques available to determine the extent of DNA
bending, however.  You might begin looking for papers by Richard Sinden or
Jan Klysik.  I think they have done some work in this area.

Yasha Hartberg
Texas A&M University
"The most beautiful thing in Tokyo is McDonald's."  Andy Warhol



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