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S Arnott

Publications and source records attributed to S Arnott.

At least 37 records · Page 2Linked to original sources
PubMed1989

Structure of the beta-form of poly d(A).poly d(U).

The crystalline beta-form of the sodium salt of poly d(A).poly d(U) trapped in oriented fibers forms a Watson-Crick base-paired, 10(1) double-helix of pitch 3.2 nm. Two molecules are present in a monoclinic unit cell apparently isomorphous with beta-poly d(A).poly d(T). The two chains in each molecule both carry C2'-endo puckered furanose rings but are conformationally not identical. The orientations of the A:U base-pairs relative to the helix-axis are distinctly different from those in classical B-DNA and the overall morphology of the duplex in which they reside resembles that of the alpha-forms of poly (purine).poly (pyrimidine) DNA duplexes previously reported.

DNA↗
PubMed1989

The synthetic DNA duplex of poly d(Abr5U).poly d(Abr5U) adopts an A-DNA-like structure.

An X-ray fiber diffraction study of the synthetic DNA duplex poly d(Abr5U).poly d(Abr5U) shows that its sodium salt adopts an unexceptional A-DNA-like structure. Similar to A-DNA, two molecules are packed in a monoclinic unit cell (a = 2.23 nm, b = 4.14 nm, c = 5.61 nm and alpha = beta = gamma = 90 degrees) of space group C2. Because of its dinucleotide chemical motif, the c-repeat is twice that in A-DNA but, notably, corresponding backbone conformation angles of adjacent nucleotides are almost identical. This is in marked contrast to many B-like conformations of polydinucleotides.

Crystallization↗
PubMed1987

Structure of the alpha-form of poly[d(A)].poly[d(T)] and related polynucleotide duplexes.

The alpha-form of poly[d(A)].poly[d(T)], observed in fibers at high (greater than 80%) relative humidity, is a 10-fold double-helical structure of pitch 3.2 nm. This new X-ray analysis shows that the two strands of the double helix are of the same kind conformationally and both B-like in containing C-2'-endo-puckered deoxyribose rings. Nevertheless, the two strands are different enough for the overall morphology of the duplex to resemble that of the heteromerous model for the drier (beta) form of poly[d(A)].poly[d(T)] in which one strand has C-2'-endo rings and the other C-3'-endo. Since the orientations of the bases in poly[d(A)].poly[d(T)] are persistently different from those of classical B-DNA it is likely that there will be local bending (about 10 degrees) at the junctions between general sequence tracts and the oligo[d(A)].oligo[d(T)] tracts that occur in some native DNAs. The conclusions about the structure of alpha-poly[d(A)].poly[d(T)] are reinforced by independent analyses of similar X-ray diffraction patterns from poly[d(A)].poly[d(U)] and poly[d(A-I)].poly[d(C-T)].

Models, Molecular↗
PubMed1986

DNA-RNA hybrid secondary structures.

DNA-RNA and DNA-DNA duplexes are even more polymorphic than observed previously. DNA-RNA hybrids can have secondary structures like A-DNA or A-RNA, but double helices of the synthetic DNA-RNA hybrids poly(dA) X poly(rU) and poly(dI) X poly(rC), respectively, form 11-fold and 10-fold double-helical structures in which the two chains have quite different conformations. Extensive X-ray fiber diffraction analyses show that in both structures the DNA chains have C-2'-endo-puckered furanose rings, while the anti-parallel RNA chains have C-3'-endo-puckered rings. The bidirectional properties of such duplexes may be important in the transfer of biological information from nucleic acids.

Base Composition↗
PubMed1986

Modelling and refinement of the crystal structure of nucleoprotamine from Gibbula divaricata.

The molecular structure of nucleoprotamine from Gibbula divaricata and its packing in oriented fibers has been modelled both to fit the X-ray diffraction pattern and to avoid steric compression. The representative model consists of 51 poly (dinucleotide) B-DNA helices with 51 poly(hexapeptide) chains associated with the major grooves. The prevailing peptide conformation is beta. The four arginine residues present are hydrogen-bonded to DNA phosphates while neutral peptides protrude into the minor grooves of neighboring nucleoprotamine molecules which are packed 2.61 nm apart in a screw-disordered, quasi-hexagonal lattice. This model reconciles a number of earlier, apparently conflicting experimental results and explains the remarkable stability of nucleoprotamines.

Animals↗
PubMed1984

Structure of a pleiomeric form of poly d(AT):poly d(AT).

A chemically simple polynucleotide duplex, poly d(AT):poly d(AT), has been trapped in a fibrous form with a complex helical secondary structure with a large (7.4 nm) axial repeat 24 nucleotides long. The motif which is repeated by the symmetry elements is a hexanucleotide in which two residues (both TpA) have the less common gauche minus conformation at C3'-O3' and consequently distinctive phosphate orientations. This reinforces earlier conclusions that PypPu nucleotides tend to have different shapes from PupPy nucleotides and that DNA surfaces may signal what base sequences lie beneath them. The morphological differences between this pleiomeric DNA polymer and closely-related, but more symmetrical allomorphs are just as great as those observed in short DNA fragments in crystals.

Base Sequence↗
PubMed1983

Hyaluronic acid: molecular conformation and interactions in the tetragonal form of the potassium salt containing extended chains.

X-ray diffraction data were used to determine the detailed crystal structure of a tetragonal form of potassium hyaluronate containing relatively extended 4-fold helical chains (rise per disaccharide h = 0.95 nm). The polysaccharide chains are left-handed (4(3] helices. Two antiparallel chains pack in a tetragonal unit cell (a = b = 0.996 nm, c = 3.788 nm) with P4(3)2(1)2 space group symmetry. The chain conformations are stabilized intramolecularly by O4-O5 hydrogen bonds across the beta(1 leads to 3) linkage and by a pair of intermolecular hydrogen bonds per disaccharide between adjacent antiparallel chains. Fourier difference synthesis revealed one potassium ion and two water molecules per disaccharide. Six polyanion oxygen atoms from three neighboring chains together with one of these water molecules form the co-ordination polyhedra. Further stability is brought about through inter- and intrachain water bridges involving both water molecules. The probable reason for the stability of this extended allomorph is discussed in terms of the preferred co-ordination geometry of the potassium ion.

Carbohydrate Conformation↗
PubMed1983

Hyaluronic acid: molecular conformations and interactions in the orthorhombic and tetragonal forms containing sinuous chains.

The conformation, packing and probable mode of cation binding have been determined for compact potassium hyaluronate chains (average rise per disaccharide h = 0.89 nm) organized in an orthorhombic unit cell (a = 1.173 nm, b = 0.925 nm, c = 3.542 nm). The space group symmetry is P2(1)2(1)2(1) and the unit cell contains two antiparallel polysaccharide chains that are disturbed 4(3) helices. Each chain is stabilized intramolecularly by four hydrogen bonds and between adjacent antiparallel chains there are two intermolecular hydrogen bonds per crystallographic tetrasaccharide repeat. Fourier difference synthesis revealed two potassium ions and two water molecules in each asymmetric unit. Both potassium ions show octahedral co-ordination geometries and link adjacent antiparallel polysaccharide chains. The water molecules provide further intermolecular association through water bridges. A comparison of this potassium hyaluronate structure with the orthorhombic and tetragonal sodium hyaluronate structures containing similar compact hyaluronate chains revealed that the apparently isomorphous orthorhombic sodium and potassium salts did not have the same packing arrangements. The relative orientations of the sinuous hyaluronate chains in the sodium and potassium salts are about 90 degrees apart. The locations of the cations and hence the coordination schemes of K+ and Na+ are therefore very different. These analyses have delineated, for the first time, how hyaluronate chains can respond differentially to two different monovalent cations.

Carbohydrate Conformation↗
PubMed1983

Hyaluronic acid double helix.

The hyaluronic acid double helix, contrary to an earlier visualization, probably incorporates extensively hydrogen-bonded chains and is pinned together by carboxyl-carboxylate hydrogen bonds and water bridges. Transient interactions between stiffened chain segments provided by the formation of double-helical loops could give rise to the characteristic viscoelastic properties of hyaluronic acid solutions.

Carbohydrate Conformation↗
PubMed1983

Dermatan sulfate: molecular conformations and interactions in the condensed state.

The molecular conformations and manner of aggregation has been determined for three allomorphs of the connective tissue polysaccharide dermatan sulfate by analysis of X-ray diffraction from oriented, polycrystalline fibers of sodium salts. One allomorph is unique among glycosaminoglycans in having right-handed (8(3)) helical chains. Two such chains pack antiparallel in a tetragonal unit cell (a = b = 1.267 nm, c = 7.353 nm) with P4(3)2(1)2 space group symmetry. The 3(2) chains of the second allomorph are organized in a trigonal unit cell (a = b = 1.460 nm, c = 2.823 nm, space group symmetry P3(2)21) containing two left-handed antiparallel polysaccharide molecules. (The chirality of this allomorph has been assumed to be the same as in other 3-fold glycosaminoglycan helices, since discrimination between 3(1) and 3(2) symmetries was found not to be possible.) The archiral 2(1) helices of the third allomorph, pack probably in an orthorhombic unit cell (a = 1.151 nm, b = 1.065 nm, c = 1.878 nm, space group symmetry P2(1)2(1)2(1)) that contains again two antiparallel polymer molecules. Each dermatan sulfate chain is stabilized intramolecularly by O3-O5 hydrogen bonds across the beta (1 leads to 4) linkage. There are two intermolecular hydrogen bonds per tetrasaccharide repeat in the tetragonal structure and two per disaccharide in the trigonal structure. Fourier difference syntheses indicated equivalents of four sodium ions per tetrasaccharide and two sodium ions per disaccharide in the tetragonal and trigonal structures, respectively. The cations are either partially or fully hydrated and link dermatan sulfate chains either intra- or intermolecularly by involving besides other polyanion oxygen atoms, carboxylate and sulfate oxygen atoms. The probable mode of packing in the orthorhombic structure indicates a pair of hydrogen bonds between adjacent antiparallel polysaccharide chains and suggests plausible cationic sites in the unit cell.

Carbohydrate Conformation↗
PubMed1983

Chondroitin 4-sulfate: comparison of the structures of the potassium and sodium salts.

Analysis of the X-ray diffraction pattern from an oriented, polycrystalline fiber of a potassium chondroitin 4-sulfate proteoglycan shows that the polysaccharide chains have a left-handed 3-fold helical secondary structure stabilized by intra- and intermolecular hydrogen bonds. Two antiparallel chains pass through each trigonal unit cell, which has dimensions a = b = 1.385 nm, c = 2.776 nm and space group symmetry P3(2)21. The cations and water molecules in the crystals are not all periodic and only one potassium ion and four water molecules per disaccharide were located by difference Fourier methods. Sodium chondroitin 4-sulfate forms an analogous structure with polyanions of similar geometry. However, the packing arrangements in the two salts are quite different, presumably because of the different co-ordination preference of K+ and Na+. Thus the relatively small differences between these two cations are greatly amplified by the idiosyncratic polymer networks they promote.

Animals↗
PubMed1983

Heteronomous DNA.

A fibrous form of poly d(A):poly d(T) has a heteronomous secondary structure which is the first to be confirmed for a polynucleotide duplex: although both chains are 10(1) helices, mutually hydrogen-bonded in the standard (Watson-Crick) fashion, each has a quite different conformation. One chain -- probably poly d(A) -- has C3'-endo-puckered furanose rings characteristic of the A family of polynucleotide secondary structures while the other -- probably poly d(T) -- has the C2'-endo-puckered rings of the B family. Since analogous heteronomous structures could be assumed by DNA-DNA or DNA-RNA duplexes containing more general base sequences the polymorphic range of polynucleotide double-helices may be even greater than we have come to suppose.

Crystallization↗
PubMed1983

Wrinkled DNA.

The B form of poly d(GC):poly d(GC) in orthorhombic microcrystallites in oriented fibers has a secondary structure in which a dinucleotide is the repeated motif rather than a mononucleotide as in standard, smooth B DNA. One set of nucleotides (probably GpC) has the same conformations as the smooth form but the alternate (CpG) nucleotides have a different conformation at C3'-O3'. This leads to a distinctive change in the orientation of the phosphate groups. Similar perturbations can be detected in other poly d(PuPy):poly d(PuPy) DNAs such as poly d(IC):poly d(IC) and poly d(AT):poly d(AT) in their D forms which have tetragonal crystal environments. This suggests that such perturbations are intrinsic to all stretches of duplex DNA where purines and pyrimidines alternate and may play a role in the detection and exploitation of such sequences by regulatory proteins.

DNA↗
PubMed1983

New wrinkles on polynucleotide duplexes.

Most fibrous polynucleotides of general sequence exhibit secondary structures that are described adequately by regular helices with a repeated motif of only one nucleotide. Such helices exploit the fact that A:T, T:A, G:C, and C:G pairs are essentially isomorphous and have dyadically-related glycosylic bonds. Polynucleotides with regularly repeated base-sequences sometimes assume secondary structures with larger repeated motifs which reflect these base-sequences. The dinucleotide units of the Z-like forms of poly d(As4T):poly d(As4T), poly d(AC):poly d(GT) and poly d(GC):poly d(GC) are dramatic instances of this phenomenon. The wrinkled B and D forms of poly d(GC):poly d(GC) and poly d(AT):poly d(AT) are just as significant but more subtle examples. It is possible also to trap more exotic secondary structures in which the molecular asymmetric unit is even larger. There is, for example, a tetragonal form of poly d(AT):poly d(AT) which has unit cell dimensions a = b = 1.71nm, c = 7.40nm, gamma = 90 degrees. The c dimension corresponds to the pitch of a molecular helix which accommodates 24 successive nucleotide pairs arranged as a 4(3) helix of hexanucleotide duplexes. The great variety of nucleotide conformations which occur in these large asymmetric units has prompted us to describe them as pleiomeric, a term used in botany to describe whorls having more than the usual number of structures. Pleiomeric DNAs need not contain nucleotide conformations that are very different from one another. On the other hand, DNAs carrying nucleotides of very different conformation must be pleiomeric. This is because 4 nucleotides of different conformation are needed to join patches of secondary structure which are as different as A or B or Z. Differences in nucleotide structures may occur also between chains rather than within chains. In poly d(A):poly d(T), the purine nucleotides all contain C3'-endo furanose rings and the pyrimidine nucleotides C2'-endo rings. Analogous heteronomous structures may exist in DNA-RNA hybrids although these duplexes are also found to have symmetrical A-type conformations.

DNA↗