Right-handed Helical Conformation Research Articles

Salt-induced Z-A-Z transition sequence in the mixed ribo-deoxyribo copolymer poly(rG-dC) X poly(rG-dC).

The left-handed helical conformation of various polynucleotides has been seen in solution at higher salt concentration than has the right-handed helical conformation of the corresponding polymer. We report here, however, studies of conformational transitions in the mixed polymer poly-(rG-dC) X poly(rG-dC). This polynucleotide appears to exist in a Z conformation under low-salt conditions, converts to an A helix at intermediate salt, and reverts to a left-handed helix at high-salt concentration.

Left-handed DNA: from synthetic polymers to chromosomes.

The interconversions between right-handed (R) and left-handed (L) helical conformations of DNA have been assessed by spectroscopic, electrophoretic, immunochemical, and enzymatic techniques. We have screened salt and solvent conditions which facilitate these transitions, as well as certain chemical modifications of the bases and backbone of defined synthetic polynucleotides. These include major and minor groove substituents as well as phosphorothioate analogues of selected phosphodiester bonds. We have established: R-L transitions in poly[d(G-C)] with iodo, bromo, methyl, and aza substitutions at the C5 position of cytosine, or phosphorothioate modification of the dGpC linkage. R-L transitions in the [d(A-C).d(G-T)]n sequence family using polymers modified as in the case of poly[d(G-C)]. The isomerizations are highly salt and temperature dependent. a possible L form of poly[d(A-T)] substituted with 2-amino adenine. the immunogenicities of constitutive and facultative Z-DNAs. the recognition specificities of different anti-Z-DNA IgGs for the spectrum of available polynucleotide probes. Some IgGs are sequence-specific. stabilization by IgG of otherwise transient left-handed conformations. anti-Z-DNA IgG binding to acid-fixed polytene chromosomes from the Diptera Drosophila, Chironomus, and Glyptotendipes. Laser scanning microscopy shows a maximal binding of 1 IgG per 3000-15,000 basepairs in acid fixed preparations. anti-Z-DNA IgG binding to negatively supercoiled plasmid, viral, phage, and recombinant closed circular DNAs. transcription from Z and Z* (associated) left-handed templates. From these and other results we propose that Z*-DNA may have important structural-functional roles in the cell.

Dependence of melittin structure on its interaction with multivalent anions and with model membrane systems*

The conformation and the aggregation state of melittin were investigated in aqueous solutions having different pH values and ionic composition as well as upon interaction with phospholipids. While circular dichroism could only show the existence, in aqueous solution, of either a random-coil or of a right-handed helical conformation, high resolution 1H and 13C n.m.r. spectra, together with the results of photon correlation spectroscopy, produced evidence in favour of a number of different well-defined structural states, depending on anion concentration and charge and on pH. In pure water at neutral pH melittin appeared to exist as a flexible random-cell monomer; in dilute NaCl a monomeric form was found which was still essentially unordered, but presented a pronounced rigidity of structure, and could be approximated to a prolate ellipsoid. When divalent anions were present (or when high ionic strengths were reached even with monovalent anions) melittin molecules associated into a compact disc-like tetramer; by 31P n.m.r., correlations could be established between the binding of phosphate ions and the variations in the structure or in the aggregation state of the polypeptide chains. As alkaline pH a helical tetramer was also found, different, however, from that formed on the presence of divalent anions at neutral pH. Upon binding to phospholipids, melittin molecules can be visualized, similarly to what happens in aqueous phosphate solutions, as consisting essentially of a bent right-handed helix, with a grouping of polar residues along one face of the molecule. The glutamine and lysine residues were strongly immobilized, while there was no n.m.r. evidence for any self-aggregation of the peptide; the ability of melittin to induce dichromate efflux from phospholipid vesicles was in fact higher when the peptide was in the monomeric state than in the tetrameric one.

Conformation of crystalline type III pneumococcal polysaccharide

The conformation of crystalline Type III pneumococcal polysaccharide, poly[(1→3)-β- d-Glc p-(1→4)-β- d-Glc p], has been studied by X-ray diffraction and stereochemical analysis. The X-ray pattern, recorded at 80 % relative humidity, led to a trigonal unit-cell, with a  b  1.028 nm, c  2.77 nm, and γ  120°. Meridional reflections on the third and the sixth layer-lines show that the chain consists of a three-fold helix, with a repeat of 0.923 nm. Conformational analysis, by the virtual-bond method, shows that one right-handed and two left-handed helices are equally favorable, on the basis of energies of isolated chains. Packing of the three helix models in the unit cell, by contact-distance criteria, ruled out the possibility of the right-handed helical conformation. One of the left-handed helices has intramolecular hydrogen-bonds O-3′...O-5 and O-2... O-6′ between the residues in the (1→4) linkage, and O-4′...O-5 between those in the (1→3) linkage. In the other left-handed helix, the O-4′...O-5 hydrogen bond is replaced by an O-2...O-2′ hydrogen bond. The choice between the two left-handed helix models is inhibited by the paucity of X-ray intensity data.

The double-helical molecular structure of crystalline b-amylose

The crystal structure of the B-polymorph of amylose appears to be based on double-stranded helices. The individual strands are in a right-handed six-fold helical conformation repeating in 20.8 Å and are wound parallel around each other. The steric disposition of O-6 is gt. The double helices pack in a hexagonal unit-cell ( a  b  18.50 Å, c (fiber repeat)  10.40 Å, γ  120°), with two helices (12 d-glucose residues) per cell. The helices are packed antiparallel and leave an open channel within a hexagonal array that is filled with water molecules. The reliability of the structure analysis is indicated by R  0.22. The structure of B-amylose is consistent with the diffraction diagrams of B-starches and accounts for the physical properties of such starches.

Molecular orbital calculations on the conformation of nucleic acids and their constituents: IX. The geometry of the phosphate group: Key to the conformation of polynucleotides?

The PCILO (ω′—ω) conformational energy maps of dimethyl phosphate constructed with different geometries of the phosphate group corresponding to the known crystal structures of U 3′p 5′A and A 2′p 5′U show that the global minimum of each map corresponds to the observed crystallographic conformation of the dinucleoside monophosphate having the same phosphate geometry. This result indicates that the conformational preferences of these relatively large molecules are determined essentially by the geometrical properties of the phosphate group. In particular it is shown in this study that the right-handed helical conformation of the dinucleoside monophosphates is favoured when the O 5′PO(I) and O 3′PO(II) valence angles have values greater than their symmetrical value (i.e. the value in the corresponding symmetrical dimethylphosphate) and that the left-handed helical conformation is favoured when these same valence angles have values smaller than their symmetrical value. A further confirmation of this rule is accomplished by analysing the phosphate group geometry in the crystal structures of diethyl phosphates. Such an analysis shows that the agreement between the observed conformations and those predicted by the rule is excellent. Ab initio calculations performed on a few selected geometries of dimethyl phosphate confirm the PCILO results. They also demonstrate that the conformation of the methyl groups has an influence on the overall stability.

Immunological recognition of polynucleotide structure.

Since the discovery of polynucleotide Phosphorylase in 1955 and the availability of synthetic polynucleotides, a vast number of physical chemical studies have been pursued with such polymers, in particular by use of optical techniques. (For review see Michelson et al., 1967). It was early shown that complementary polynucleotides readily interacted to give DNA type double-stranded helical complexes. Since then, secondary structure in single strands, though less well defined, has been amply explored, as well as formation of triple-stranded complexes under certain conditions. All of these “natural” polymers and polymer complexes adopt a right-handed helical conformation in aqueous solution, and though left-handed structures have been proposed (these do indeed exist in polynucleotides containing L-ribose instead of D-ribose), no rigorous evidence of their existence in natural polynucleotides has been provided. Although the overall geometry is thus right-handed helical, a variety of geometrically distinct forms are known to exist, for example the A, B and C forms of DNA and the A form of double-helical RNA. In addition, chemical and physical studies have shown that synthetic polynucleotide complexes possess different absolute geometries in terms of double helix, and indeed two extreme DNAs, poly dAT from crab, and DNA from Micrococcus lysodeikticus (72% GC) show quite different structures.

Conformational studies of -glucans.

AbstractA study of the effect of linkage on the possible conformations of di‐and polysaccharides of α‐D‐glucose and also the probable intramolecular hydrogen bonds has been made. The differences in the nature of linkage is shown to effect the energetically preferred conformations; (1 → 2) linkages lead only to righthanded helical conformations, (1 → 3) linkages lead to extended as well as both left and righthanded helical conformations; (1 → 4) linkages lead to both right‐and lefthanded wide helical conformations. The possible hydrogen bonds between adjacent residues are also dependent on the nature of the linkage. A comparison of the conformational data of α‐D‐glucans with those of β‐D‐glucans has indicated that the favored conformations and hydrogen bonds between contiguous residues in the chain are influenced by the configuration at the anomeric carbon atom in all the three types of polysaccharides. From the energy calculations a probable conformation (ϕM = −10°, ψM = −30°, ϕN = −23°, ψN = −19°) has also been proposed for crystalline mycodextran in conformity with x‐ray data. This conformation contains two types of hydrogen bonds between contiguous residues one between 0–2 and 0–3 atoms at (1 → 4) linkage and the other between 0−2 and 0–4 atoms at (1 → 3) linkage in the chain. The conformation of maltose unit (−10°,−30°) that is likely to occur in the crystalline mycodextran coincides with the minimum energy conformation of maltose.

CONFORMATIONAL STUDIES ON SYNTHETIC POLY-α-AMINO ACIDS: THE HELICAL SENSE OF POLY-L-TRYPTOPHAN: OPTICAL ROTATORY DISPERSION STUDIES

The synthesis of high molecular weight (100 000 to 200 000) polymers and copolymers of L-tryptophan and γ-benzyl-L-glutamate is reported. The optical rotatory dispersion (o.r.d.) of these polypeptides is recorded in the wavelength range 540–320 mμ and the b0 values of the Moffitt equation, using λ0 = 212ν, are listed. Poly-L-tryptophan has a b0 value of +570 in dimethylformamide (DMF). A linear relationship exists between this value, b0 values of copolymers of various ratios of L-tryptophan and γ-benzyl-L-glutamate, and the value of− 670 found for poly-γ-benzyl-L-glutamate. The o.r.d. curve of a poly-L-tryptophan film, in the 330–200 mμ wavelength range, reveals two positive Cotton effects in the 270–290 mμ region and a large negative Cotton effect at 233 mμ. Thus, despite the positive b0 value, these data prove that poly-L-tryptophan, in DMF, has the right-handed helical conformation. Hypochromicity was found for the tryptophanyl residue in the helical polypeptide. The rotatory contribution of chromophores, such as tryptophan or coenzymes, when bound asymmetrically to a protein, can be very significant, and caution is advised in the interpretation of such o.r.d. curves.

Wave Functions and Energy Eigenvalues for the Polytetrafluoroethylene Chain

The paper reports on a quantum mechanical investigation of an isolated polytetrafluoroethylene molecule. The purpose of this investigation is twofold: to find the energy gap between filled and empty electronic bands and to determine the energy required to change the conformation of the molecule. For reasons of simplicity, the carbon atoms are assumed to have the planar zigzag conformation in the ground state of the molecule. Molecular wave functions are constructed from Bloch sums taken along the four rows of fluorine atoms. The basis functions used are Gaussian approximations to 2p and 3s atomic orbitals. The suitability of this choice is tested in a preliminary calculation of the dissociation energy of the hydrogen fluoride molecule. In polytetrafluoroethylene, the molecular orbitals form bands. The energy gap between the filled 2p band and the empty 3s band is calculated as 10.07 ev, suggesting negligible intrinsic semiconduction. The width of the 2p band is 0.0625 ev, signifying that chain conformation may change easily at room temperature, for example from a right-handed helical conformation to the conformation of the opposite hand.