D.W.L. Hukins

Optimised parameters for A-DNA and B-DNA.

Abstract Atomic coordinates and other stereochemical parameters are presented for the A and B conformations of DNA. The molecular structures presented have the most probable values of bond-lengths, bond-angles and furanose ring conformations as defined by accurate X-ray crystallographic analyses of relevant monomers. Conformation-angles have values that provide the best (least-squares) fit with the X-ray diffraction data observed from the polymers themselves. The major difference between A- and B-DNA is in the conformation of the furanose ring that is (C3- endo ) for A and (C3- exo ) for B.

Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers

Abstract The molecular structure of the B form of DNA has been refined using the 3 A resolution X-ray diffraction intensities (from crystalline fibers of its lithium salt) and supplementary stereochemical data. Atomic positions have been determined with a precision of a few tenths of an Angstrom unit. The best model is similar to earlier ones but unlike them has no undesirable stereoehemical features, apparently as a result of having the furanose rings in a standard C3-exo conformation. The correctness of the base-pairing scheme has also been investigated. Alternatives to the Watson-Crick scheme can be rejected decisively. The strategy used to test alternative molecular models is of general application.

Structural details of a double-helix observed for DNAs containing alternating purine and pyrimidine sequences☆

Abstract Double-stranded DNA molecules in which purine and pyrimidine nucleotide residues alternate along each chain can assume a novel, right-handed, 8-fold helical form with an axial rise per residue of 3.03 A. The furanose rings have the standard C3-exo conformation. The bases are positioned unusually with respect to the helix axis even though they connect the two antiparallel chains through purinepyrimidine hydrogen bonds of the Watson & Crick (1953) type. The molecules assume an unprecedentedly dense packing in which each has four nearest neighbors with center-to-center distances of only 17 A. The molecular geometry also supports assignment of a structural rather than transcriptional role to satellite DNA in biological systems.

Optimised parameters for RNA double-helices

Abstract Atomic coordinates, obtained by analysis of the X-ray fiber diffraction data from synthetic RNA double-helices, are presented for A-RNA and A′-RNA. (A′-RNA is produced by increasing the salt content in fibers of A-RNA which is the conformation already observed for viral RNA double-helices.) The most probable values of bond-lengths and bond-angles (derived from accurate X-ray diffraction analyses of monomer crystal structures) were assigned to the polymer models which also have ribose rings in the standard C3- endo conformation. Conformation-angles have the experimental values which provide the (least-squares) best fit with the X-ray diffraction data from highly crystalline fibers of poly(A)·poly(U) (for A-RNA) and poly(I)·poly(C) (for A′-RNA). Both models are right-handed, anti-parallel, double-helices with Watson-Crick base-pairs and similar overall conformations. However, A-RNA is an eleven-fold helix whereas the A′-RNA helix is twelve-fold.

Structures of synthetic polynucleotides in the A-RNA and A′-RNA conformations: X-ray diffraction analyses of the molecular conformations of polyadenylic acid · polyuridylic acid and polyinosinic acid · polycytidylic acid

Abstract X-ray dinraction patterns snow that syntnetic RNA A aoubie-helices, poly(A) · poly(U) and poly(I) · poly(C), are 11-fold and can exist in fibers in a crystalline form isomorphous with · -A-RNA from reovirus. The data from poly(A) · poly(U) were used to refine molecular parameters (and calculate their estimated standard deviations) for A -RNA; the values of these parameters are very similar to those obtained from independent refinements using data from α- and β- A -RNA (reovirus), but for the more numerous poly (A) · poly(U) data the parameters are defined more precisely. Poly(I) · poly(C) and poly(A) · poly(U) can undergo a salt-induced transition to the 12-fold helices of A ′-RNA. Molecular parameters of A ′-RNA, with their estimated standard deviations, were obtained from a refinement using X-ray diffraction data from poly(I) · poly(C). The reported structure of the synthetic DNA-RNA hybrid poly(I) · poly(dC) is not significantly different from A ′-RNA. A ′-RNA and A ′-RNA are very similar to each other, and to A -DNA, in having antiparallel polynucleotide chains, C3- endo puckered furanose rings and Watson-Crick base pairs about 4 A from the helix axis. The most obvious difference between these molecules is in the “tilt” of the base pairs. Structural similarities between poly(A) · poly(U) and poly(I) · poly(C) are consistent with their comparable ability to induce Interferon; the tendency of poly(A) · poly(U) to form a triple helix under conditions when poly(I) · poly(C) merely undergoes the A to A ′ transition may explain why it has sometimes been found to be less effective. The homopolymer sequences of poly(A) · poly(U) and poly(I) · poly(C) may help to stabilize A -type conformations. Since homopolymer stretches in DNA appear to act as control sites for RNA transcription, the possible enhanced stability of their A conformations is consistent with a suggestion that DNA might adopt the A conformation during transcription.

Hyaluronic acid: molecular conformations and interactions in two sodium salts.

Abstract A detailed structure for the tetragonal form ( a = b = 0.989 nm, c , fibre axis, = 3.394 nm) of sodium hyaluronate has been obtained by analysing X-ray fibre diffraction data using new molecular modelling techniques. Two polysaccharide chains pass through each unit cell, one at the corner and one at the centre. The chains are anti-parallel to one another. Each chain is a left-handed, 4-fold helix of disaccharide units. There are intramolecular hydrogen bonds stabilising each glycosidic linkage. Octahedrally co-ordinated sodium ions link, by O … Na + … O bridges, neighbouring polysaccharide chains that are further linked by hydrogen bonds. No double-helix model (as originally proposed for this structure) has been found to be free of unacceptable non-bonded contacts or to fit the diffraction intensities as closely. The tetragonal form, which is stable at zero relative humidity, contains no detectable water molecules. At higher relative humidities a related orthorhombic form is observed in which only the a dimension of the lattice is different ( a = 1.153 nm, b = 0.989 nm, c = 3.386 nm). In this form the hyaluronate helix is 2-fold with tetrasaccharide units conformationally similar to the 4-fold helix of the tetragonal form. The Na + … O binding and hydrogen bonds lost on expansion of the tetragonal lattice are all replaced in the orthorhombic structure by bridges through water molecules, four of which associated with each tetrasaccharide.

Conformation of keratan sulphate.

Abstract X-ray diffraction patterns from stretched films of keratan sulphate, isolated from bovine cornea, indicate that the molecules are twofold helices with an axial rise per disaccharide residue of 0.945 nm. These helices are oriented with their twofold screw axes parallel and about equally spaced, but are not further organized into regular crystalline arrays. Computer methods were used to construct a molecular model with the observed symmetry and axial rise per disaccharide residue, with standard bond lengths, bond angles and pyranose ring conformations and with a hydrogen bond of length 0.270 nm between O(3) of N-acetylglucosamine and O(5) of galactose. This model has no unacceptably short non-bonded interatomic distances. The intensity distribution of the diffraction pattern calculated from the co-ordinates of the model is in reasonable agreement with the observed intensity distribution. This keratan sulphate model is an extended polysaccharide chain fringed with charged sulphate side groups, and is similar to those that have already been reported for chondroitin sulphates and dermatan sulphate, paralleling the similarities in covalent structure and biological occurrence among these substances.

Mucopolysaccharides: Comparison of Chondroitin Sulfate Conformations with Those of Related Polyanions

X-ray diffraction shows that chondroitin 6-sulfate, and some further rulfated derivatives, can occur in two ordered structures in stretched films. Both structures contain single helices with similar projected disaccharide lengths (9.6 and 9.8 angstroms) but with very different turn angles between successive disaccharides (120 and 45 degrees). In contrast, coaxial double helices of hyaluronates and t-carrageenates have shorter projected disaccharide lengths (8.5 and 8.9 angstroms).

Dermatan sulfate and chondroitin 6-sulfate conformations

Abstract X-ray diffraction patterns show that dermatan sulfate in oriented, crystalline films occurs as two or three or eight-fold helices. The two-fold helix has a greater axial rise per disaccharide residue [ h = 9.6 A ] than the corresponding chondroitin 6-sulfate helix [ h = 9.3 A ] . Three-fold dermatan sulfate and chondroitin 6-sulfate helices both have h = 9.5 A . Consequently the α-L-iduronate residues in dermatan sulfate helices have the C1 chair conformation like β-D-glucuronate in chondroitin 6-sulfate. Since the eight-fold dermatan sulfate helix has h = 9.3 A rather less than the eight-fold chondroitin 6-sulfate helix [ h = 9.8 A ] the possibility of α-L-iduronate 1C chairs cannot be ruled out for it. Computer methods have been used to produce molecular models. In these the polysaccharide chains are almost linear. Each backbone conformation can accommodate a variety of arrangements of charged side groups.