DNA STRUCTURE PUZZLE NUMBER 2

Clive Delmonte clivedelmonte at c-i-delmonte.freeserve.co.uk
Sun Oct 10 06:27:19 EST 1999


DNA STRUCTURE PUZZLE NUMBER 2

Optical Diffraction Compared With X-Ray Diffraction for B-DNA

It was Franklin's famous diffraction photograph of B-DNA (3), set out in the
website, shown to him by Wilkins, that Watson sketched on the train back to
Cambridge to rejoin Crick.

One of Wilkins' collaborators, A R Stokes (4), produced probably the first
optical diffraction prediction of the pattern arising from a true
side-by-side helical structure, set out in the website, this one having 8
repeat units per full turn. This true side-by-side structure mirrors that
found in Ref. 1(Puzzle #1)) by STM.

Stokes' optical diffraction pattern would seem to resemble closely
Franklin's X-ray diffraction pattern of B-DNA.

In the same paper (4), Stokes, from his work on the Fourier transform for a
helix, showed that, defining as "delta" the angle between an arm of the
"helical cross" and the Y-axis (meridian):

tan delta = helical pitch / helical circumference

Applying this result to Franklin's photograph of B-DNA, delta is measured as
40 degrees, and, with a pitch of 3.34 nm, the helical diameter is found to
be some 1.3 nm.  It seems that Stokes' result was never applied to B-DNA
diffraction photographs by Crick, Watson, Wilkins, Franklin or Stokes.

Even in later work with better definition, for example, from Wilkins' group
on Li-DNA, included in the website, we see a similar value of delta.

For a supposed double helical diameter of 2 to 2.2 nm, delta should be 28 -
26 degrees respectively, far removed from the actual values of 40 - 41.

The helical diameter of 1.3 nm, found from Stokes' equation applied to
Franklin's & Wilkins' photographs, coincides with the STM value of 1.3 nm
measured by Lee et al. (Puzzle #1, Ref. 1), recorded in their Figure 3d, and
accords with the Watson-Crick base pair width of 1.1 nm which itself
determines the sugar-phosphate chain diameter set out in Ref. 2.
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3 Molecular Configuration in Sodium Thymonucleate; R.E. Franklin &
R.G.Gosling; Nature Vol 171 (1953) 740-741
4 The Theory of X-ray Fibre Diagrams; A.R. Stokes; Prog. Biophys. & Biophys.
Chem. Vol 5 (1955) 140-167
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Clive Delmonte

For a view of all the DNA Structure Puzzles
and the DNA publications, please refer to:
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