Molecular structure of nucleic acids
A structure for deoxyribose nucleic acid
We wish to suggest a structure for the salt of deoxyribose
nucleic acid (D.N.A) this structure has novel features which are of
considerable biological interest.
A structure for nucleic acid has already been proposed by
pauling and corey. They kindly made their manuscript available to us in advance
of publication. Their model consists of three intertwined chains, with the
posphates near the fibre axis, and the bases on the outside. In our opinion,
this structure is unsatisfactory for two reasons:
1.
We believe that the material which gives the
x-ray diagrams is the salt, no the free acid. Without the acidic hydrogen atoms
it is not clear what forces would hold the structure together, especially as
the negatively charged phosphates near the axis will repel each other.
2.
Some of the van der waals distances appear to be
too small.
Another three-chain structure has also been suggested by
fraser (in the press). In his model the phosphates are on the outside and the
bases on the inside, linked together by hydrogen bonds. This structure as described
is rather ill-defined, and for this reason we shall not comment on it.
We wish to put forward a radically different structure for
the salt of deoxyribose nucleic acid. This structure has two helical chains
each coiled round the same axis (see diagram). We have made the usual chemical
assumptions, namely, that each chain consists of phosphate diester groups
joining β-D-deoxy-ribofuranose
residues with 3’, 5’ linkages. The two chains (but not their bases) are related
by a dyad perpendicular to the fibre axis. Both chains follow right-handed
helices, but owing to the dyad the sequences of the atoms in the two chains run
in opposite directions. Each chain loosely resembles furberg’s model no 1 :
that is, the bases are on the inside of the helix and the phosphates on the
outside. The configuration of the sugar and the atoms near it is close to
furberg’s ‘standars configuration’, the sugar being roughly perpendicular to
the attached base. There is a residue on each chain every 3 4 A in the
z-direction. We have assumed an angle of 36’ between adjacent residues in the
same chain, so that the structure repeats after 10 residues on each chain, that
is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10 A.
As the phosphates are on the outside, cations have easy access to them.
The structure is an open one, and its water content is
rather high. At lower water contents we would expect the bases to tilt so that
the structure could become more compact.
The novel feature of the structure is the manner in which
the two chains are held together by the purine and pyrimidine bases. The planes
of the bases are perpendicular to the fibre axis. They are joined together in
pairs, a single base from one chain being hydrogen-bonded to a single base from
the other chain, so that the two lie side by side with identical
z-co-ordinates. One of the pair must be a purine and the other of pyrimidine
for bonding to occur. The hydrogen bonds are made as follows: purine position 1
to pyrimidine position 1; purine position 6 to pyrimidine position 6.
If it is assumed that the bases only occur in the structure
in the most plausible tautomeric forms ( that is, with the keto rather than the
enol configurations) it is found that only specific pairs of bases can bond
together. These pairs are : adenine (purine) with thymin (pyrimidine), guanine
(purine) with cytosine (pyrimidine).
In other words, if an adenine forms one member of a pair, on
either chain, then on these assumptions the otheeer member must be tymine :
similarly for guanine and cytosine. The sequence of bases on a single chain
does not appear to be restricted in any way. However, if only specific pairs of
bases can be formed, it follows that if the sequence of bases on one chain is
given, then sequencce on the other chain is automatically determined
It has been found experimentally 3,4 that the ratio of the
amounts of adenine to thymine, and the ratio of guanine to cytosine, are always
very close to unity for deoxyribose nucleic acid
It is probably impossible to build this structure with a
ribose sugar in place of the deoxyribose, as the extra oxygen atom would make
too close a van der waals contact.
The previously published X-ray data 5,6 on deoxyribose
nucleic acid are insufficient for a rigorous test of our structure. So far as
we can tell, it is roughly compatible with the experimental data, but it must
be regerded as unproved until it has been checked against more exact results. Some
of these are given in the following communications. We were not aware of the
details of the results presented there when we devised our srtucture, which
rest mainly though not entirely on published experimental data and stereochemical
arguments.
It has not escaped our notice that the specific pairing we
have postulated immediately suggest a possible copying mechanism for the
genetic material
Full details of the structure, including the conditions
assumed in building it, together with a set of co-ordinates for the atoms, will
be published elsewhere.
We are much indebted to Dr. Jerry Donohue for constant
advice and criticism, especially on inter-atomic distances. We have also been
stimulated by a knowladge of the general nature of the unpublished experimental
results and ideas of Dr. M. H. F. Wilkins, Dr. R. E. Franklin and their
co-worker at king’s collage, london
Medical research council unit for the Study of the molecular
structure of biological systems, Cavendish laboratory, cambrige.
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