Rengaswami Chandrasekaran

Polymorphism of DNA double helices

Abstract Native DNA duplexes in fibers exist usually in one of three well-known ( A , B and C ) forms depending on relative humidity, type of cations and the amount of retained salt. To determine the precise influence of these factors and the effect of base composition, as well as base sequence, on DNA secondary structure, X-ray diffraction methods have been used to study all four synthetic DNA duplexes with repeated dinucleotide sequences, eight of the 12 with repeated trinucleotide sequences and seven analogues in which guanine was replaced with hypoxanthine. The results indicate that there are at least six additional allomorphs denoted by B ′, C ′, C ″, D , E and S . The B ′ form ( h = 0.329 nm) observed for poly(dA) · poly(dT), poly(dI) · poly(dC) and poly[d(A-I)] · poly[d(C-T)] is a minor variant of the traditional B form ( h = 0.338 nm) of native DNA. The two C -like forms C ′ for poly[d(A-G-C)] · poly-[d(G-C-T)] and poly[d(G-G-T)] · poly[d(A-C-C)] and C ″ for poly[d(A-G)] · poly-[d(C-T)] have, respectively, 9 1 and 9 2 symmetries which reflect repetition of trinucleotide and dinucleotide sequences, respectively. Although isocompositional with poly(dA) · poly(dT), the existence of the rather different D form (8 1 ) for poly[d(A-T)] · poly[d(A-T)] or for poly[d(A-A-T)] · poly[d(A-T-T)] is a clear demonstration of the sequence effect. The I · C pair generally mimics an A · T pair, but poly[d(I-I-T)] · poly[d(A-C-C)] provides a new ( E ) form with approximately 15 2 screw symmetry and with 〈 h 〉 = 0.325 nm and 〈 t 〉 = 48 dg per nucleotide. The S form (6 5 ) observed for poly[d(G-C)] · poly[d(G-C)] and poly[d(A-C)] · poly[d(G-T)] is an unusual left-handed polydinucleotide helix and is accessible to any alternating purine-pyrimidine sequence. In it the two nucleotides have quite different conformations and involve syn purine and anti pyrimidine nucleosides.

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.

Cation interactions in gellan: An x-ray study of the potassium salt

Gellan belongs to a new generation of nonsulfated, microbial, texturing polysaccharides of potential interest to the food industry. The influence of monovalent cations on its molecular geometry has been investigated by X-ray diffraction analysis of oriented fibers of the potassium salt. The molecule forms a parallel, half-staggered, double helix in which each polysaccharide chain is a left-handed, 3-fold helix of pitch 5.63 nm. The potassium ion is coordinated to the carboxylate group, which is in turn involved in interchain hydrogen-bonds to stabilize the duplex. There are two such duplexes, packed antiparallel to each other, cross-linked by a network of duplex-water-duplex interactions, in the trigonal unit cell, a = b = 1.575 nm, and c = 2.815 nm. The present study not only confirms the correctness of the basic structure of gellan reported previously for the lithium salt but also furnishes a clear insight into the critical interactions taking place between the polymer chains, cations, and water molecules which are of importance for industrial utilization.

The influence of calcium ions, acetate and l-glycerate groups on the gellan double-helix

Abstract A computer-assisted linked-atom least-squares program has been used to visualize the crystal structure of calcium gellan and to examine the ability of acetate and l -glycerate groups in native gellan to sustain the doublehelix and to maintain the potassium gellan crystal packing. The results explain the strong and brittle gelation behavior at low ionic strength of calcium gellan and suggest that the weak and rubbery gelation behavior of native gellan is perhaps due to the l -glycerate groups.

Molecular architectures and functional properties of gellan gum and related polysaccharides

Abstract Certain linear and branched polysaccharides produced by unrelated species of bacteria are grouped in the gellan gum family because of their conserved backbone structures. All have excellent rheological properties and, thus, are useful in industrial applications. Physicochemical investigations of these polysaccharides in solution and structural studies of them in the solid state using X-ray diffraction have provided mutually complementary results. The study double-helix morphology that is characteristic of gellan gum prevails in other members of the gum family in spite of the presence of substituents and side chains. Association between double helices is facilitated by ions and water molecules. The observed physical properties of solutions and gels made with members of the gellan gum family can be directly rationalized at the molecular level in terms of the interactions taking place between the polymer helices

The crystal structure of gellan

Abstract Gellan is a nonsulfated, anionic, extracellular polytetrasaccharide secreted by the bacterium Auromonas elodea . It is potentially useful in the food industry because of its gel-forming properties. The molecular basis of these properties had been investigated by X-ray diffraction analysis of oriented fibers, but an exhaustive study by Upstill et al. in 1986 produced no molecular model with a remotely acceptable fit to the observed X-ray intensities. We describe here a successful re-examination of the crystal structure of gellan; the gellan chains have backbone conformations different from those previously considered. Two left-handed, 3-fold helical chains are organized in parallel fashion in an intertwined duplex in which each chain is translated half a pitch ( p = 5.64 nm) with respect to the other. The duplex is stabilized by interchain hydrogen bonds at each carboxylate group. There are two molecules in each trigonal unit cell ( a = 1.56 nm and c = 2.82 nm).

The molecular structure of kappa-carrageenan and comparison with iota-carrageenan

Abstract The ordered conformation of kappa-carrageenan molecules in condensed but well-hydrated systems has been investigated by refining stereochemically plausible models to fit the continuous X-ray diffraction data obtained from oriented fibers. In the best model, the molecules are coaxial duplexes comprising right-handed, 3-fold helical chains of pitch 25.0 A. As with iota-carrageenan, the chains are parallel but their juxtaposition in kappa-carrageenan is significantly different since they are offset from the half-staggered arrangement by a 28° rotation and a 1.0-A translation. Alternative models (single helices, coaxial duplexes containing 6-fold chains, noncoaxial dimers, and mixtures of single and double helices) are quite incompatible with the diffraction data. Some antiparallel, coaxial duplex models approach the best model either in stereochemical plausibility or fit with the diffraction data, but none is as convincing overall as the best (parallel-stranded) model.

Structure of the single-stranded polyribonucleotide polycytidylic acid

Abstract X-ray fibre diffraction studies have shown that at pH 7.0 polyribocytidylic acid (poly(C)) can adopt a single-stranded, right-handed, 6-fold helical structure with an axial rise per residue of 0.311 nm. The furanose rings have the C-3′-endo conformation. The other conformation angles of this structure are also remarkably similar to those observed in A -type double-stranded polynucleotide structures with the exception of θ[C-4′,z.sbnd;C-3′,z.sbnd;O-1,z.sbnd;P], which adopts a value very close to the monomer average. There is no hydrogen bonding between bases. The molecular structure appears to be stabilised primarily by base-stacking interactions and the crystal structure by hydrogen bonds between ribose hydroxyl groups.

Roles of potassium ions, acetyl and l-glyceryl groups in native gellan double helix: an X-ray study

Native gellan, the natural form of the polysaccharide excreted by the bacterium Pseudomonas elodea, has a tetrasaccharide repeating unit that contains L-glycerol and acetate ester groups, and forms only weak and elastic gels. Based on X-ray diffraction data from well oriented and polycrystalline fibers of its potassium salt, the crystal structure of native gellan, including ions and water, has been determined and refined to a final R-value of 0.17. The molecule forms of a half-staggered, parallel, double helix of pitch 5.68 nm which is stabilized by hydrogen bonds involving the hydroxymethyl groups in one chain and both carboxylate and glyceryl groups in other. Two molecules are packed in an antiparallel fashion in a trigonal unit cell of side a = 1.65 nm. Although the gross molecular morphology and packing arrangements are isomorphous with those observed in the crystal structure of potassium gellan, which is devoid of any substitutions, native gellan exhibits exceptional changes in its ion binding characteristics with respect to gellan. In particular, the L-glyceryl groups do not allow the gellan-like coordinated interactions of the ions and the carbohydrate groups, within and between double helices, which are necessary for strong gelation. These results at the molecular level explain, for the first time, the differences in the behavior of the polymer with and without substitutions.

The Structure of B-DNA in Oriented Fibers

Native, general sequence B-form DNA in uniaxially oriented fibers is a ten-fold helix with identical antiparallel strands: this is to say the molecular symmetry is 2 2 10(1). The diffraction patterns indicate that local variations, however significant, must be modest. This is true also for the lithium salt of calf thymus DNA in fibers that are polycrystalline as well as oriented. The contents of its orthorhombic unit cells are arranged with P2(1)2(1)2(1) symmetry which permits the molecular symmetry to be merely two-fold. The molecular structure of DNA in such conditions resembles, conformationally and molecularly, that of B-type DNA in oligonucleotide single crystals and in oriented polycrystalline fibers of polyoligonucleotides, and therefore provides a basis for evaluating the variations that may be due to sequence effects in polyoligonucleotides in fibers and oligonucleotides in single crystals.