Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

The crystal structure of the dipotassium salt of uridine 5'-diphosphate

C9H12N2Ot2P22-. 2K + .3H20 is orthorhombic, P2~2~2p with a = 18.977 (5), b - 22.597 (6), c = 8.995 (2) A, Z = 8. The structure was refined to R = 0.059 for 2587 observed reflexions. The two molecules of the asymmetric unit have very similar conformations with a 2'- endo sugar pucker and a folded pyrophosphate chain. They form a dimer, coordinated by the K + ions but without direct bridging between the base and the pyrophosphate within each individual molecule. One uracil base has the keto-enol and the other the diketo form. The extended structure shows alternating hydrophobic and hydrophilic regions.

Structure of Relativistic States

QCD factorization in the Bjorken limit allows to separate the long-distance physics from the hard subprocess. At leading twist, only one parton in each hadron is coherent with the hard subprocess. Higher twist effects increase as one of the active partons carries most of the longitudinal momentum of the hadron, x -> 1. In the Drell-Yan process \pi N -> \mu^- mu^+ + X, the polarization of the virtual photon is observed to change to longitudinal when the photon carries x_F > 0.6 of the pion. I define and study the Berger-Brodsky limit of Q^2 -> \infty with Q^2(1-x) fixed. A new kind of factorization holds in the Drell-Yan process in this limit, in which both pion valence quarks are coherent with the hard subprocess, the virtual photon is longitudinal rather than transverse, and the cross section is proportional to a multiparton distribution. Generalized parton distributions contain information on the longitudinal momentum and transverse position densities of partons in a hadron. Transverse charge densities are Fourier transforms of the electromagnetic form factors. I discuss the application of these methods to the QED electron, studying the form factors, charge densities and spin distributions of the leading order |e\gamma> Fock state in impact parameter and longitudinal momentum space. I show how the transverse shape of any virtual photon induced process, \gamma^*(q)+i -> f, may be measured. Qualitative arguments concerning the size of such transitions have been previously made in the literature, but without a precise analysis. Properly defined, the amplitudes and the cross section in impact parameter space provide information on the transverse shape of the transition process.

Conformational studies of the triphenylphosphazenyl side chain in cyclophosphazenes. I. Crystal and molecular structure of N3P3C15(NPPh3)

The title compound, C t8H~sC15NaP4, crystallizes in the monoclinic space group P2~/n with a = 20.14 (2), b = 8.69 (1), c = 14.92 (2) A, fl = 98.8 (3) ° , Z = 4. The structure was determined from visual data and refined to R = 0-069 for 1450 reflections. The cyclophosphazene ring is non-planar. The exocyclic NPPh 3 group exhibits type I conformation [R. A. Shaw (1975). Pure Appl. Chem. 44, 317-341] in which the N-P bond is perpendicular to the adjacent P-CI bond.

Structure of a cyclic water tetramer in a nucleotide crystal host and a hypothetical model for water cluster growth

Structure of a cyclic water tetramer in channels (pores) formed by self-assembly of N6-methyl-5'-AMP center dot Na-2 molecules is described and a hypothetical model is proposed for growth of water clusters. (C) 2010 Elsevier B.V. All rights reserved.

X-ray studies on crystalline complexes involving amino acids and peptides. XXI. Structure of a (1:1) complex between L-phenylalanine and D-valine

CsHllNO2.C9HilNO2, Mr = 282.3, P1, a = 5.245 (1), b = 5.424 (1), c = 14.414 (2) A, a = 97.86 (1), fl = 93-69 (2), y = 70-48 (2) °, V= 356 A 3, Z = 1, O m = 1-32 (2), Dx = 1.32 g cm-3, h(Mo Ka) = 0-7107 A, g = 5-9 cm-1, F(000) = 158, T= 298 K, R=0.035 for 1518 observed reflections with I>2tr(I). The molecules aggregate in double layers, one ayer made up of L-phenylalanine molecules and the other of D-valine molecules. Each double layer is stabilized by interactions involving main-chain atoms of both types of molecules. The interactions include hydrogen bonds which give rise to two head-to-tail sequences. The arrangement of molecules in the complex is almost the same as that in the structure of DL-valine (and DL-leucine and DL-isoleucine) except for the change in the side chain of L molecules. The molecules in crystals containing an equal number of L and O hydrophobic amino-acid molecules thus appear to aggregate in a similar fashion, irrespective of the precise details of the side chain.

Structure of disocium uridine 5'-Phosphate heptahydrate

Na2[CgHllN2OgP].7H20, M r = 494.0,orthorhombic, C222~, a = 22.880 (7), b = 8.877 (3),c = 19.592 (9) A, Z = 8, V = 3979.2 A 3. The Cu Ka intensity data consisted of 1005 unique reflections. Final R -- 14.5%. This nucleotide shows no unusual conformational features. The uracil base has an anti conformation about the glycosidic bond (tpo o = 44.4°). The furanose ring conformation is C(2')-endo,gauchegauche with tpo o = -75.5 ° and ~Poc = 49"6°.

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

Structure of the Indian southwesterly pre-monsoon and monsoon boundary layers: Observations and numerical simulation

Characteristics of pre-monsoon and monsoon boundary layer structure and turbulence were studied in New Delhi and Bangalore, India during the summer of 1987. Micrometeorological towers were installed and instrumented at these locations to provide mean and turbulent surface layer measurements, while information on the vertical structure of the atmosphere was obtained using miniradiosondes. Thermal structures of the pre-monsoon and monsoon boundary layers were quite distinct. The daytime, pre-monsoon boundary layer observed over New Delhi was much deeper than that of the monsoon boundary layer observed over Bangalore and at times was characterized by multiple inversions. Surface, turbulent sensible heat fluxes at both sites were approximately the same (235 and 200 Wm−2 for New Delhi and Bangalore, respectively). Diurnal variations in the monsoon boundary layer at Bangalore were more regular compared to those under pre-monsoon conditions at New Delhi. One-dimensional numerical simulations of the pre-monsoon boundary layer using a turbulent energy closure scheme show good agreement with observations.

A novel metal binding mode of a pyrimidine nucleotide. Crystal structure of [Cu(5′-UMP)(im)2(H2O)]·4H2O

X-ray analysis of the ternary complex [Cu(5′-UMP)(im)2(H2O)]·4H2O, where 5′-UMP uridine-5′-monophosphate and IM = imidazole, reveals a novel metal binding mode of pyrimidine nucleotide through the ribose group.

An unusual axial co-ordination of phenolate oxygen to copper(II): crystal structure of chloro(2-[bis(2-pyridylmethyl)aminomethyl]-4-nitrophenolato)copper(II)

A tripod ligand possessing two pyridine moieties and a phenolato group as pendants forms a mononuclear complex with an axial copper(II)–phenolate co-ordination in a square-pyramidal environment.