Re: [ccp4bb]: how to retrieve structural info. from the local base-pair parameters?

[Michael Sierk <mls5w@virginia.edu>]

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Steve,

See Olson, et al (http://www.pnas.org/cgi/content/abstract/95/19/11163) 
for a quantitative description of what the parameters mean.  You can 
actually use the data from the paper to calculate how distorted your 
DNA is in units of kT.  One easy thing to do is to plot Roll, Slide, 
and Twist (and Tilt, Rise, and Shift) along the sequence and see if 
there are any peaks that stand out.  You can also run Curves to get an 
idea of how bent your DNA is.

Good luck,
Mike Sierk

On Friday, August 30, 2002, at 04:18  PM, Q. Steven Xu wrote:

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>
> I used the CURVES and X3DNA to perform structure analysis on a DNA
> molecule and got detailed base-pair parameters like slide, rise, tilt,
> roll, etc. But those valuses don't make much sense to me since i have 
> no
> experience on DNA structure although I do know what those parameters 
> mean.
> My question is how I can tell from those parameters if the DNA is 
> bended,
> if there is any unstacking base pair, if DNA is somewhat unwinding or
> whatever questions like these. Is there any quantitative criteria for
> these parameters or just qualitative ones to make judgements?
>
> Any comments, references, tutorials are welcome. Many thanks.
>
> regards,
> Steve
>
>
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Michael Sierk, Postdoctoral Fellow        email: mls5w@virginia.edu
Biochemistry & Molecular Genetics Dept.   Phone(W):  (434) 924-2821
P.O. Box 800733                  			    (H):  (434) 970-2268
University of Virginia
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