W. J. Pigram

Neutron fibre diffraction study of DNA hydration

Interactions with water are crucial to the conformation assumed by the DNA double helix. The location of water around the D conformation has been investigated in a neutron fibre diffraction study which shows that water is ordered in the minor groove of the DNA. The D conformation is important since its occurrence is limited to specific DNA base pair sequences which have been identified as functionally significant. This study is of particular interest because the D conformation has not been reported in single crystal studies of oligonucleotides.

A high angle neutron fibre diffraction study of the hydration of the A conformation of the DNA double helix.

A high angle neutron fibre diffraction study of the distribution of water around the A-form of DNA has been performed using the diffractometer D19 at the Institut Laue-Langevin, Grenoble. These experiments have exploited the ability to replace H2O surrounding the DNA by D2O so that isotopic difference Fourier maps can be computed in which peaks are identified with the distribution of water in the unit cell. All peaks of significant height have been accounted for by four families of water molecules whose positions and occupancies have been determined using least squares refinement. The coordinates of the water peaks making up each family do not deviate significantly from a regular helical arrangement with the same parameters as the DNA. Two of these families are of particular interest. The first consists of water molecules in the major groove linking successive charged phosphate oxygens along the polynucleotide chains. The second is associated with bases in the major groove and forms a central core of density along the helix axis. These two families provide a layer of hydration lining the interior wall of the major groove leaving a central channel to accommodate cations. The relationship between these observations and conformational stability is discussed.

THE LOCATION OF WATER AROUND THE DNA DOUBLE-HELIX

Abstract The diffractometer D19 at the ILL has been used to locate water around the DNA double-helix in fibres of the polynucleotide poly[d(A-T)].poly[d(A-T)]. Neutron fibre diffraction data were recorded to a resolution of 3 A first when the DNA was surrounded by D 2 O and second when it was surrounded by H 2 O.

High angle neutron fibre diffraction studies of the distribution of water around the D form of DNA

Abstract The instrument D19 at the Institut Laue-Langevin, Grenoble, has been used to undertake neutron fibre diffraction studies of the location of water around the D form of the DNA double helix. These studies clearly show the distribution of water in the small and large grooves of the molecule and, together with information from X-ray studies on the location of cations around the molecule, provide new information on the factors which help to stabilise this form of DNA.

DNA Hydration Studied by Neutron Fiber Diffraction

The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institut Laue-Langevin. Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformational transitions in the DNA double-helix.

Time-Resolved X-Ray Fibre Diffraction Studies of Structural Transitions in the DNA Double-Helix Using the Daresbury SRS

X-ray fibre diffraction has played a crucial role in the determination of the three-dimensional stereochemistry of deoxyribonucleic acid (DNA) (Watson and Crick, 1953; Wilkins, Stokes and Wilson, 1953; Franklin and Gosling, 1953). Early studies showed that the DNA molecule consists of two polynucleotide strands which can assume a variety of highly regular helical conformations. Of particular significance was the observation that the conformations assumed were essentially independent of the biological origin of the DNA and hence of the particular genetic information coded in the sequence of adenine, thymine, guanine and cytosine bases along each polynucleotide strand (Hamilton et al., 1959). The double-helical model for DNA proposed by Watson and Crick resolved in a very elegant way the paradox of how a molecule with the very high degree of regularity indicated by the x-ray fibre diffraction data could also code within its structure a great variety of genetic information. In this model the repeating unit is an average nucleotide with the sugar-phosphate chain which links together successive bases having the same conformation irrespective of the base to which it is attached. Since the sugar-phosphate chains lie on the outside of the molecule its overall appearance and hence the way neighbouring molecules can pack together in crystalline fibres is highly regular.