On the application of direct methods to oligonucleotide crystallography

The direct methods program SAYTAN was applied to simulated data at various resolutions from three oligonucleotides. Success in solving the structures was found to depend more upon the resolution of the data than upon errors in the data or the complexity of the structure. Collecting the data at a reduced temperature has little effect, unless it alters the mosaicity of the crystal or changes the resolution of the data. The presence of a heavy atom dramatically improved the phase refinement, particularly at low resolution.

X-ray diffraction from DNA fibres under tension

When DNA fibres are stretched during drying, the polymer undergoes a conformational transition. We present quantitative results from X-ray diffraction studies on such fibres held at various ambient relative humidities. These indicate that the molecules are arranged in arrays which are crystalline in projection down the fibre axis. The packing can be explained in terms of a hexagonal cell with a lattice parameter, a, of approximately 13 A which varies with humidity. The patterns contain meridional intensities at 1/3.4 A(-1) and 1/6.5 A(-1), a strong off-meridional intensity at Z=1/5.6 A(-1) and diffuse scatter at Z=1/28 A(-1).

Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing

Molecular dynamics simulations with simulated annealing are performed on polyamine-DNA systems in order to determine the binding sites of putrescine, cadaverine, spermidine and spermine on A- and B-DNA. The simulations either contain no additional counterions or sufficient Na+ ions, together with the charge on the polyamine, to provide 73% neutralisation of the charges on the DNA phosphates. The stabilisation energies of the complexes indicate that all four polyamines should stabilise A-DNA in preference to B-DNA, which is in agreement with experiment in the case of spermine and spermidine, but not in the case of putrescine or cadaverine. The major groove is the preferred binding site on A-DNA of all the polyamines. Putrescine and cadaverine tend to bind to the sugar-phosphate backbone of B-DNA, whereas spermidine and spermine occupy more varied sites, including binding along the backbone and bridging both the major and minor grooves.

Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing

Molecular dynamics simulations with simulated annealing are performed on polyamine-DNA systems in order to determine the binding sites of putrescine, cadaverine, spermidine and spermine on A- and B-DNA. The simulations either contain no additional counterions or sufficient Na+ ions, together with the charge on the polyamine, to provide 73% neutralisation of the charges on the DNA phosphates. The stabilisation energies of the complexes indicate that all four polyamines should stabilise A-DNA in preference to B-DNA, which is in agreement with experiment in the case of spermine and spermidine, but not in the case of putrescine or cadaverine. The major groove is the preferred binding site on A-DNA of all the polyamines. Putrescine and cadaverine tend to bind to the sugar-phosphate backbone of B-DNA, whereas spermidine and spermine occupy more varied sites, including binding along the backbone and bridging both the major and minor grooves.

On the application of anomalous scattering in oligonucleotide crystallography

Simulated anomalous-scattering differences, at wavelengths between 1.5 and 5.5 A, were used with MULTAN to locate P atoms in an oligonucleotide hexamer. The success of the method depended heavily on the level of errors in the data. With error-free data most or all P atoms were located at all wavelengths. With noisy data, the best results were obtained by refining the phases associated with the largest values of |DeltaF|/sigma(|DeltaF|) rather than with the largest values of |DeltaF|. In this case a few of the P-atom positions could be located, with the best results occurring at wavelengths between 3.0 and 4.0 A. Further improvements were gained by reducing the values of the thermal parameters of the P atoms. MULTAN figures of merit had limited success in indicating the best phase sets, but a small improvement was gained by modifying the procedure for selecting those reflections used in the calculation of PSIZERO.

Structure factor calculations for a side-by-side model of B-DNA

In this paper, the side-by-side model of DNA proposed by Premilat and Albiser is investigated. The axial repeat of the model is equal to the c-axis repeat in the observed B-DNA unit cell in fibres. However, the model does not pack into the unit cell as efficiently as the B-DNA double helix does, nor is it as successful as the double helix in predicting the observed Bragg amplitudes. When the azimuthal orientations and the relative axial displacements of the two molecules in the unit cell are allowed to take general values, the best crystallographic R factor for the side-by-side model is 43.43% compared with 34.33% for the double helix. If constraints consistent with the accepted B-DNA space group, P2(1)2(1)2(1), are applied, the best R factors are 45.53% for the side-by-side model and 34.51% for the double helix. Therefore, the side-by-side model can be rejected as a possible conformation for B-DNA in crystalline fibres.

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.

Time-resolved X-ray diffraction studies of the B in equilibrium D structural transition in the DNA double helix

Because of the relation between topology and function, there has been much interest in the structural transitions of the various conformations of DNA polymers. The x-ray fiber diffraction analysis system at the Daresbury Synchrotron Radiation Source was used to study the reversible transition between the B and D forms of the synthetic DNA poly[d(A-T)].poly[d(A-T)]. The gradual progression of conformations between these two forms indicates that the DNA double helix does not undergo a change of handedness during this transition.

Facilities for solution scattering and fibre diffraction at the Daresbury SRS

The small-angle scattering facility at Daresbury has been constructed for diffraction studies of a wide range of naturally occurring and synthetic materials. The high brightness of the SRS is combined with focusing optics, resulting in exposure times that can be two or three orders of magnitude less than those required on a conventional source. Spacings of 2000 Å in the vertical direction and 300 Å in the horizontal direction can be observed, while the resolution between diffraction orders is 5000 and 600 Å. In addition, preliminary results have been obtained on a double-crystal diffractometer that has a resolution, in one dimension, of better than 26 000 Å. For high-angle fibre diffraction studies, a camera with pinhole collimation has been constructed. Examples from solution scattering and fibre diffraction are used to illustrate the performance of these facilities.

X-ray diffraction from the side-by-side model of DNA

An intriguing topological problem posed by the double-helical Watson-Crick model of DNA is that of unwinding the intertwined strands during replication. Several workers have recently proposed novel side-by-side (SBS) structures for DNA. In all these models the two strands are joined by complementary Watson-Crick base pairs and the antiparallel polynucleotide strands alternate between short segments of right- and left-handed helix, thus both reducing the amount of intertwining and alleviating the unwinding problem. We show here that there are unacceptable discrepancies between the observed diffraction pattern of B-DNA and that calculated for the original SBS structure. We also describe a simple modification of this model which resolves some of the more serious discrepancies. However, the agreement is still markedly inferior to that obtained for a Watson-Crick model of DNA.