DNA Structure: Puzzle Number 9

clive delmonte clived at ndirect.co.uk
Mon Dec 7 06:56:13 EST 1998


Suwalski & Traub (14) studied a fibre of the DNA-polyarginine complex by
X-ray diffraction.  Their diffraction pattern shows "pronounced streaks" in
a hexagonal lattice of side 4.15nm and they remarked that the equatorial
reflections followed h x h + h x k + k x k = 3n.

This pattern of equatorial presences is equivalent to that of Fuller et al.
(Puzzle Number 4, ref.6) where such presences follow h-k=3n in a cell whose
side can be reduced.  Squaring (h-k) and subtracting from the expression in
the previous paragraph, there is a differerence of 3hk, a quantity always
divisible by 3.  Therefore Suwalski & Traub's value of 'a' can reduced by
root 3.

Suwalski and Traub decided that their pattern of systematic absence could be
explained by postulating axial translations of the molecules equal to c/3.

Marvin et al. (Puzzle Number 4, ref. 5) considered that a random axial
translation of their molecules of c/2 would account for the streaks on their
layer lines.

Now, the very same diffraction pattern of Suwalski and Traub with
DNA-polyarginine was reindexed on an orthogonal net by Fita et al. (15) in a
unit cell of approximate section 2.6nm x 3.6 nm (16) where equatorial
reflections followed h+k=2n.

Langridge et al. (Puzzle Number 4, ref. 7) have shown that this pattern of
presences would allow the halving of the long side of the cell section.

Fita et al. considered that the pattern of systematic absences in their
orthogonal net indicated that the axial translation of the molecules was
c/4.

So Suwalski & Traub considered that the fibre had axial displacements of the
molecules of c/3 in a hexagonal net, and Fita et al. found the axial
displacement to be c/4 in an orthogonal net.  But there was only one single
fibre and only one diffraction pattern.

Therefore, whether a hexagonal or orthogonal array is chosen, the axial
dispacement can only have one value.  The value common to both analyses is
c/2, but this is deducible from the layer line streaks and not from the
patterns of systematic absence.

Therefore the patterns of systematic absence in both the hexagonal and
orthogonal nets should be taken to show that, for both indexing schemes, a
smaller unit cell is the right choice, with a random axial displacement of
c/2.

However, if the unit cell sizes are reduced accordingly, the double helix
can no longer be fitted into the reduced dimensions of the original cells.


As we have seen in the earlier Puzzles, a true side-by-side duplex, where
each helix has a diameter of about 1.3nm, and, in this case, has its grooves
at least partially filled with poly-arginine, will fit the new, reduced unit
cells.



14        A Comparative X-ray Study of a Nucleoprotamine & DNA Complexes
with Polylysine & Polyarginine; M. Suwalski & W. Traub; Biopol. Vol 11
(1972) 2223 - 2231


15        X-ray Diffraction Study of DNA Complexes with Arginine Peptides
and Their Relation to Nucleoprotamine Structure; I. Fita, J.L. Campos, L.C.
Puigjaner & J.A. Subirana; J Mol Biol Vol 167 (1983) 157 - 177


16        X-ray Diffraction Studies of Nucleoprotamine Structure; P. Suau &
J.A. Subirana; J Mol Biol Vol 117 (1977) 909 - 926
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