function that defines DNA?

rmw rwadkins at cbmse.nrl.navy.mil
Wed May 31 16:49:25 EST 1995


In article <01HR4LSS8Z3E8Y6JO2 at VAX.CS.HSCSYR.EDU>
HIGGINSS at VAX.CS.HSCSYR.EDU ("SEAN M. HIGGINS") writes:

> Would someone direct me towards a function[f(x)] that
> represents DNA.  I don't need anything elaborate; a simple
> B-form major groove ribbon / quarter-pipe type model 
> would do just fine.
> 
> S. Higgins 
> higginss at vax.cs.hscsyr.edu

Probably the simplest model of intact DNA double helices
is that proposed by Arnott & Hukins (1972) Biochem. Biophys.
Research Comm. 47: 1504-1509.  This is "perfect" A or B-form
DNA modeled in cylindrical polar coordinates, with all base
pairs 3.38 angstroms above each other and the base pairs
perfectly flat (B form).  This is an all-atom model. You could 
generate an approximate model by placing any object at 
coordinates X = r*cos(theta), Y = r*sin(theta), Z = Z.
(These are in terms of cylindrical coordinates) where
r is the distance from the cylinder axis (about 9 angstroms
on average for phosphate groups, 7 angstroms for sugar atoms,
3-4 angstroms for base atoms), with the angle between 
successive residues 36 degrees (i.e., theta = theta_initial +
36), and the distance along the cylinder axis between residues
of 3.38 angstroms (Z = Z_initial + 3.38).  This produces a 
single strand.  You need to reverse theta and Z to generate
double stranded DNA.
--Randy




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