DNA Structure Puzzle Number 3 - X-Ray Diffraction from Fibres of Li-DNA

Clive Delmonte clivedelmonte at c-i-delmonte.freeserve.co.uk
Sun Oct 17 02:57:34 EST 1999


PUZZLE NUMBER 3 - X-Ray Diffraction from Fibres of Li-DNA


Marvin et al. (5) drew fibres of the lithium salt of C-DNA in both hexagonal
and orthorhombic lattices. In a hexagonal lattice of side 3.5 nm.,
systematic absences followed (-h+k) =/=3n for l=0, and (-h+k)=3n when l=1 or
2.

Streaks were found on several layer lines in both lattices and could be
explained by molecules having a random axial translation of c/2, without
using the systematic absences, according to Marvin et al.

Fuller et al. (6) state that such a pattern of systematic absence allows the
choice of a hexagonal unit cell of side reduced by root 3. Marvin et al.
chose the larger unit cell, large enough to accommodate a double helix.

If we elect to reduce the unit cell size, a double helix cannot be
accommodated, and we find that the maximum, outer helix diameter which can
be acommodated to be:

(3.5 nm / root 3) x sin 60 x 2/3 = 1.2 nm

In an orthorhombic lattice, where Marvin et al. found a=3.22 nm and b=2.02
nm, large enough to accommodate a double helix, they report that systematic
equatorial absences follow h+k=2n+1. This pattern of absence is reported by
Langridge et al. (7) to allow the halving of the long side to form a new
reduced unit cell. In a reduced orthorhombic cell with a=2.02 nm and
b=1.61nm, a double helix cannot be accommodated, and we find that the
maximum outer diameter of a helix which can be accommodated is now 1.3 nm.

In both hexagonal and orthorhombic lattices, the observed streaks in the
patterns could result from a random axial displacement of duplexes of c/2,
according to Marvin et al. If we elect to explore the implications of a
random axial translation of c/2, utilising the layer line streaks as
evidence, we are able to use the systematic absences in both lattices to
choose a smaller unit cell in each case.

Applying Stokes' equation to the helical cross of Li DNA in the Langridge
paper (7), we find delta = 41 degrees and the helical diameter to be 1.22
nm.

A DNA helical diameter of 1.2 to 1.3 nm is therefore deducible directly from
the STM work of Lee et al. (Ref. 1) (and many other AFM & STM studies set
out in Ref. 48), or by applying Stokes' equation to Franklin's B-DNA
diffraction pattern (Ref. 3) and to diffraction from Li DNA in the C form
(7), or from James and Mazia's surface film of B-DNA (Puzzle 20 still to
come).

A very wide range of entirely separate experiments suggests that the helical
diameter of the major diffractors (the sugar-phosphate chains) is 1.2 to 1.3
nm. This dimension is dictated solely by the Watson-Crick base pair width of
1.1 nm in a true side-by-side model (see Refs. 2 & 4).

---------------------------------------------
1 Scanning Tunnelling Microscopy of Nucleic Acids; G. Lee, P.G. Arscott,
V.A. Bloomfield & D. Fennell Evans; SCIENCE Vol 244 (1989) 475 - 477

2 Towards A New Structural Molecular Biology, by Clive Delmonte, ISBN 0
9512276 0 2 (1991)

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

 5 The Molecular Configuration of Deoxyribonucleic Acid. III. X-ray
Diffraction Study of the C form of the Lithium Salt; D.A. Marvin, M.
Spencer, M.H.F. Wilkins & L.D. Hamilton; J Mol Biol Vol 3 (1961) 547 - 565

6 Molecular and Crystal Structures of Double-helical RNA; W. Fuller, F.
Hutchinson, M. Spencer & M.H.F. Wilkins; J Mol Biol Vol 27 (1967) 507 - 524

7 The Molecular Configuration of Deoxyribonucleic Acid. I.; R. Langridge,
H.R. Wilson, C.W. Hooper, M.H.F. Wilkins & L.D. Hamilton; J Mol Biol Vol 2
(1960) 19-37
----------------------------------------------------------
Clive Delmonte

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