DNA Structure: Puzzle Number 12

clive delmonte clived at ndirect.co.uk
Tue Dec 15 02:28:21 EST 1998


Aaron Klug (18, page 373) has reported that Rosalind Franklin was working on
a sugar-phosphate helical diameter of 1.1nm, deduce from her Pattersons, at
the time that Watson & Crick formulated their idea of a double helix.
Franklin's value of 1.1 nm resonates with the values of 1.2 nm to 1.3 nm
outer helical diameters recorded, for example, in Puzzle 1(ref. 1 and other
AFM &STM refs.), Puzzle 2 (ref. 2), Puzzle 3 (ref. 4) and Puzzle 4 (ref. 7).

Most importantly, and unknown to Franklin at that time,1.1 nm is also the
width of the Watson-Crick base pair. Supposing, as a working hypothesis,
that base pairs are connected across the two (antiparallel) helices recorded
by Lee et al. (Puzzle 1, ref. 1), then the geometry requires each
sugar-phosphate helix to adopt the same diameter as the base pair width.
This leads us directly to dimensions for the duplex of about 1.2nm x 2.1nm,
values deduced already from the experimental results of James & Mazia
(Puzzle 3, ref. 4).

Wilkins et al. (19) analysed the diffraction pattern of B-DNA:  "...The
strong equatorial reflection....suggests that the helices have a maximum
diameter of approximately 2.0 nm....On the sixth, seventh and eighth layer
lines the maxima correspond to a helix of diameter approximately 1.2nm...";

and, further, Wilkins et al. write (20):...In particular, it appears that
the helix, when viewed along the fibre axis, may not be quite round in
section but elliptical."

So Wilkins' group finds a helical diameter of 1.2 nm in an elliptical
section of major diameter approximately 2.0 nm, which reinforce closely
similar, elliptical values of 1.2 nm  and 2.1 nm deduced directly from the
1953 paper by James & Mazia.

These days, the structure of oligonucleotides is deduced from diffraction
from true crystals and purports to show double helical structures.

But there is a slight snag with this process.  There are no oligonucleotide
structural solutions based upon direct methods on their own, because direct
methods require data at a very high resolution, about 0.1 nm, and the
highest oligonucleotide resolution to date is about 0.15 nm.  All the
oligonucleotide studies reported to date involve feeding the double helix,
directly or indirectly, into the computational algorithms along with the raw
data.

Typical examples of this practice, which just happen to lie randomly to
hand, would include

B-DNA:  (21, page 8863): " ...starting with a standard B-form DNA as
established from fiber diffraction..."

Z-DNA:  (22, Note 19):  The 3 x 3 matrix, generating the coordinates of the
two strands, defines a double helix.

B-DNA:  (23, page 1374):The initial coordinates of the ....decamer were
those of the idealized canonical B-DNA..."

A-DNA: (24, page 806): "...a model... was constructed in the A-form using
fibre coordinates..."

B-DNA:   (25, page 1162): "We decided to solve and refine the structure
using coordinates from idealized, fibre-diffraction B-DNA..."

So, if a double helix is fed into the algorithm, naturally a double helix
comes out.

The Puzzle for today is this.   The true side-by-side structure visualised
by Lee et al. (Puzzle 1, ref.1) in their STM research shows identically zero
plectonaemic turns over any and all lengths and has a helical diameter of
some 1.3 nm for each helix, in accord with results from many independent
experiments.   If this model is fed as B-DNA into the computational
algorithms shall we get out a structure with a comparable
crystallographic residual to those resulting from a double helical input ?

The whole body of oligonucleotide structures presently deposited at
Brookhaven would seem to be compromised by the prior acceptance of a
plectonaemic structure for duplex DNA in the A, B and Z forms which even
early fibre diffraction studies and other, especially recent,
non-crystallographic work does not much support.


18        The Path to the Double Helix; R. Olby: Macmillan

19        Molecular Structure of DNA; M.H.F. Wilkins, A.R. Stokes and H.R.
Wilson; Nature Vol 171 (1953) 738 - 740

20        Helical Structure of Crystalline DNA; M.H.F. Wilkins, W.E. Seeds,
A.R. Stokes & H.R. Wilson; Narure Vol 172 (1953) 759 - 762

21        The Structure of B-helical CGATCGATCG and Comparison with
CCAACGTTGG; K. Grzeskowiak, K. Yanagi, G.G. Prive & R.E. Dickerson; J Biol
Chem Vol 266 (1991) 8861 - 8883

22        Left-handed Double Helical DNA: Variations in the Backbone
Conformation; A.H.-J. Wang, G.J. Quigley, F.J. Kolpak, G. van der Marel,
J.H. van Boom & A. Rich; Science Vol 211 (1981) 171 - 176

23        Interaction of Berenil with the EcoRI Dodecamer (CGCGAATTCGCG) in
Solution Studies by NMR; A.N. Lane, T.C. Jenkins, T. Brown & S. Neidle;
Biochemistry Vol 30 (1991) 1371 - 1385

24        G.T Base-pairs in a DNA Helix: The Crystal Structure of
d(GGGGTCCC); G. Kneale, T. Brown, O. Kennard & D. Rabinovich; J Mol Biol Vol
186 (1985) 805 - 814

25        Molecular Structure of the B-DNA Dodecamer d(CGCAAATTTGCG); K.J.
Edwards, D.G. Brown, N. Spink, J.V. Skelly & S. Neidle; J Mol Biol Vol 226
(1992) 1161 - 1173

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