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W J Pigram

Publications and source records attributed to W J Pigram.

15 recordsLinked to original sources
PubMed1996

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.

Crystallography↗
PubMed1992

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.

DNA↗
PubMed1989

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.

DNA↗
PubMed1986

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.

DNA↗
PubMed1983

Conformational transitions in the synthetic polynucleotide poly[d(G-C)] . poly[d(G-C)] double-helix.

Conditions are described for observing by X-ray fibre diffraction the A, B and S conformations of the poly[d(G-C)] . poly[d(G-C)] double-helix and also a new form designated as B". For fibres with an appropriate ionic content, transitions between these conformations can be induced by varying the relative humidity of the fibre environment. With increasing relative humidity the transitions B" leads to A leads to S leads to B occur. However, reducing the relative humidity does not result in a simple reversal of these transitions. If the relative humidity is reduced rapidly, a B leads to A transition is observed followed by an A leads to B" transition, but if it is reduced slowly, the transition is from B to S. Once the S form has been assumed, further reduction in the relative humidity does not result in a transition to the A form. The S form emerges as a particularly stable form of the poly[d(G-C)] . poly[d(G-C)] double-helix. From the point of view of its relationship to the classical A and B forms, the S form of poly[d(G-C)] . poly[d(G-C)] is shown to exhibit similarities to the D form of poly[d(A-T)] . poly[d(A-T)].

Humidity↗
PubMed1983

Conformational transitions in oriented fibres of the synthetic polynucleotide poly[d(AT)].poly[d(AT)] double helix.

The synthetic polynucleotide poly[d(AT)].poly[d(AT)] is of interest in studies of the relationship between nucleic acid structure and function. In particular, A + T-rich regions in DNA double helices have been invoked as centres for controlling the transcription of genetic information. Here we describe conditions for observing by X-ray fibre diffraction the A, B, C and D conformations of Na-poly[d(AT)].poly[d(AT)], and for inducing transitions between these conformations. The D form emerges as a particularly stable conformation; once assumed, it persists over a wide range of variation in the relative humidity of the fibre environment. Further, while transitions between the B and D conformations are readily reversible, transitions between A and D are much more complex.

Nucleic Acid Conformation↗
PubMedDate not supplied

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.

DNA↗