Molecular and crystal structure of deoxyguanosine 5'-phosphate

RECENT crystallographic studies of the dinucleosides ApU (ref. 1) and GpC (ref. 2) have given experimental proof for the base pairing arrangement proposed by Watson and Crick for the DNA double helix3. Another striking feature of this structure relates to the torsional angle about the C5'-C4' bond in the phosphate−sugar backbone chain. In the Crick and Watson model4, this conformation is gauche−trans (GT). Crystal structures of 5'-nucleotides, dinucleosides and dinucleotides so far studied, however, have shown only the gauche−gauche (GG) conformation about this bond. The GG conformer is also the only one found in the refined models of the proposed structure of the double helical nucleic acids and polynucleotides5−7. The only nucleotide with a GT conformation is 6-azauridine-5'-phosphate8 which is not a normal monomer unit of nucleic acids. It is also reported that 5'-dGMP assumes preferentially GT conformation in solution9.

Population Expansion and Genetic Structure in Carcharhinus brevipinna in the Southern Indo-Pacific

Background:Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna), a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa. Methods and Findings:Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025). While two metrics of genetic divergence (ΦST and FST) revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717–0.03508, p values ≤ 0.0013; pairwise FST South Africa vs New South Wales = 0.04056, p = 0.0008). Evidence for fine-scale genetic structuring was also detected along Australia’s east coast (pairwise ΦST = 0.01328, p < 0.015), and between south-eastern and northern locations (pairwise ΦST = 0.00669, p < 0.04).Conclusions: The Indian Ocean represents a robust barrier to contemporary gene flow in C. brevipinna between Australia and South Africa. Gene flow also appears restricted along a continuous continental margin in this species, with data tentatively suggesting the delineation of two management units within Australian waters. Further sampling, however, is required for a more robust evaluation of the latter finding. Evidence indicates that all sampled populations were shaped by a substantial demographic expansion event, with the resultant high genetic diversity being cause for optimism when considering conservation of this commercially-targeted species in the southern Indo-Pacific.

Crystal and molecular structure of a dimethyl sulphoxide complex with lanthanum nitrate, La(NO3)3.4(CH3)2SO

Abstract is not available.

Study of Structural Stability and Electronic Structure of Nonstoichiometric CdS Nano Clusters from First Principles

Structural stability of small sized nonstoichiometric CdS nano clusters between zincblende and wurtzite structures has been investigated using first-principles density functional calculations. Our study shows that the relative stability of these two structures depends sensitively on whether the surface is S-terminated or Cd-terminated. The associated band gap also exhibits non-monotonic behavior as a function of cluster size. Our findings may shed light on contradictory reports of experimentally observed structures of CdS nano clusters found in the literature.

Charge distribution, dipole moments and molecular structure of some organogermanium compounds

Formal charge distributions in, and the electric dipole moments of, a few simple organogermanium compounds have been evaluated by the method of R. P. Smith et al. [J. Amer. Chem. Soc., 73(1951) 2263]. The difference between the experimental and calculated moments in the case of alkylhalogermanes is explained in terms of the pπ—dπ back bonding effect outweighing the electron releasing effect. In unsaturated compounds, the differences are attributed to possible mesmeric effects involving the expansion of the germanium valence shell.

Molecular and crystal structure of deoxyguanosine 5'-phosphate

RECENT crystallographic studies of the dinucleosides ApU (ref. 1) and GpC (ref. 2) have given experimental proof for the base pairing arrangement proposed by Watson and Crick for the DNA double helix3. Another striking feature of this structure relates to the torsional angle about the C5'-C4' bond in the phosphate−sugar backbone chain. In the Crick and Watson model4, this conformation is gauche−trans (GT). Crystal structures of 5'-nucleotides, dinucleosides and dinucleotides so far studied, however, have shown only the gauche−gauche (GG) conformation about this bond. The GG conformer is also the only one found in the refined models of the proposed structure of the double helical nucleic acids and polynucleotides5−7. The only nucleotide with a GT conformation is 6-azauridine-5'-phosphate8 which is not a normal monomer unit of nucleic acids. It is also reported that 5'-dGMP assumes preferentially GT conformation in solution9.

Deriving structural information from non-coding ribonucleic acids by mass spectrometry

The purpose of this study is to describe the development of application of mass spectrometry for the structural analyses of non-coding ribonucleic acids during past decade. Mass spectrometric methods are compared of traditional gel electrophoretic methods, the characteristics of performance of mass spectrometric, analyses are studied and the future trends of mass spectrometry of ribonucleic acids are discussed. Non-coding ribonucleic acids are short polymeric biomolecules which are not translated to proteins, but which may affect the gene expression in all organisms. Regulatory ribonucleic acids act through transient interactions with key molecules in signal transduction pathways. Interactions are mediated through specific secondary and tertiary structures. Posttranscriptional modifications in the structures of molecules may introduce new properties to the organism, such as adaptation to environmental changes or development of resistance to antibiotics. In the scope of this study, the structural studies include i) determination of the sequence of nucleobases in the polymer chain, ii) characterisation and localisation of posttranscriptional modifications in nucleobases and in the backbone structure, iii) identification of ribonucleic acid-binding molecules and iv) probing of higher order structures in the ribonucleic acid molecule. Bacteria, archaea, viruses and HeLa cancer cells have been used as target organisms. Synthesised ribonucleic acids consisting of structural regions of interest have been frequently used. Electrospray ionisation (ESI) and matrix-assisted laser desorption ionisation (MALDI) have been used for ionisation of ribonucleic analytes. Ammonium acetate and 2-propanol are common solvents for ESI. Trihydroxyacetophenone is the optimal MALDI matrix for ionisation of ribonucleic acids and peptides. Ammonium salts are used in ESI buffers and MALDI matrices as additives to remove cation adducts. Reverse phase high performance liquid chromatography has been used for desalting and fractionation of analytes either off-line of on-line, coupled with ESI source. Triethylamine and triethylammonium bicarbonate are used as ion pair reagents almost exclusively. Fourier transform ion cyclotron resonance analyser using ESI coupled with liquid chromatography is the platform of choice for all forms of structural analyses. Time-of-flight (TOF) analyser using MALDI may offer sensitive, easy-to-use and economical solution for simple sequencing of longer oligonucleotides and analyses of analyte mixtures without prior fractionation. Special analysis software is used for computer-aided interpretation of mass spectra. With mass spectrometry, sequences of 20-30 nucleotides of length may be determined unambiguously. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Sequencing in conjunction with other structural studies enables accurate localisation and characterisation of posttranscriptional modifications and identification of nucleobases and amino acids at the sites of interaction. High throughput screening methods for RNA-binding ligands have been developed. Probing of the higher order structures has provided supportive data for computer-generated three dimensional models of viral pseudoknots. In conclusion. mass spectrometric methods are well suited for structural analyses of small species of ribonucleic acids, such as short non-coding ribonucleic acids in the molecular size region of 20-30 nucleotides. Structural information not attainable with other methods of analyses, such as nuclear magnetic resonance and X-ray crystallography, may be obtained with the use of mass spectrometry. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Ligand screening may be used in the search of possible new therapeutic agents. Demanding assay design and challenging interpretation of data requires multidisclipinary knowledge. The implement of mass spectrometry to structural studies of ribonucleic acids is probably most efficiently conducted in specialist groups consisting of researchers from various fields of science.

The study of genetic diversity and population structure of the Korean fleshy shrimp, Fenneropenaeus chinensis, using newly developed microsatellite markers

The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.

Isotope shifts and hyperfine structure in the 555.8-nm S-1(0) -> P-3(1) line of Yb

We apply our technique of using a Rb-stabilized ring-cavity resonator to measure the frequencies of various spectral components in the 555.8-nm 1S0-->3P1 line of Yb. We determine the isotope shifts with 60 kHz precision, which is an order-of-magnitude improvement over the best previous measurement on this line. There are two overlapping transitions, 171Yb(1/2-->3/2) and 173Yb(5/2-->3/2), which we resolve by applying a magnetic field. We thus obtain the hyperfine constants in the 3P1 state of the odd isotopes with a significantly improved precision. Knowledge of isotope shifts and hyperfine structure should prove useful for high-precision calculations in Yb necessary to interpret ongoing experiments testing parity and time-reversal symmetry violation in the laws of physics.

Aromatic amines and their derivatives. Part 3. The synthesis and crystal structure of 4,4-NN-tetramethyl-NN-dinitroso-2,2-methylenedianiline

The synthesis of 4,4,N,N-tetramethyl-NN-dinitroso-2,2-methylenedianiline (1) by the route p-MeC6H4NH2+ HCHO + OH–(p-MeC6H4NMe)2CH2(7b); (7b)+ acid at 70 °C 4,N-dimethyl-6-(N-methyl-p-toluidinomethyl)aniline (4b); (4b)+ acid at 130 °C 4,4,NN-tetramethyl-2,2-methylenedianiline (3b); (3b)+ HNO2(1), is described. Aspects of the 1H n.m.r. spectra of the above and related compounds are discussed. A crystal-structure analysis of compound (1) shows one of the N-nitroso-groups to be disordered with the endo-form being in preponderance (4 : 1) over the exo-form. The other N-nitroso-group is exclusively exo in the solid state. There is little or no resonance between the benzene ring and the nitroso-group attached to the ring, the two groups being almost perpendicular to each other. In one of the N-nitroso-groups, the nitrogen atom deviates significantly from the plane of the benzene ring to which it is attached. Both amide nitrogen atoms show some pyramidal character.

Crystal and molecular structure of allo-4-hydroxy-L-proline dihydrate

allo-4-Hydroxy-L-proline crystallizes from an aqueous solution as the dihydrate. The crystals are orthorhombic, space group P212121, with a=7.08 (2), b=22.13 (3), c= 5"20 (2) A,. The structure was solved by direct methods and refined by block-diagonal least squares. The final R for 733 observed reflexions is 0.054. The molecule exists as a zwitterion with hydroxyl and carboxyl groups cis to the pyrrolidine ring. The latter is puckered at the fl-carbon atom, which deviates by -0.54 A, from the best plane formed by the four remaining atoms. The molecules are held together by a network of hydrogen bonds, the water molecules playing a dominant role in the stability of the structure.

Crystal and molecular structure of 15-bromolongibornane-8,9-dione

The crystal and molecular structure of the title compound (1) has been determined by the heavy-atom method from 1038 observed three-dimensional photographic data. Crystals are orthorhombic, with a = 20.07 ± 0.02, b= 10.05 ± 0.02, c= 7.31 ± 0.01 Å, space group P212121, with Z= 4. The structure was refined by block diagonal leastsquares to R 0.099. The conformation of the norbornane moiety is discussed. The seven-membered ring portion of the molecule adopts an approximate chair conformation. The packing of the molecules in the crystal is mainly a consequence of van der Waals interactions.

The crystal and molecular structure of the amino terminal tetrapeptide of alamethicin. A novel 310 helical conformation

The molecular structure of N-benzyloxycarbonyl-α-aminoisobutyryl-prolyl-α-aminoisobutyryl-alanyl methyl ester (Z-Aib-Pro-Aib-Ala-OMe), the amino terminal tetrapeptide of alamethicin is reported. The molecule contains two consecutive β-turns with Aib-Pro and Pro-Aib at the corners, forming an incipient 310 helix. This constitutes the first example of an X2-Pro3 β-turn in the crystal structure of a small peptide.

Structural studies of analgesics and their interactions. III. The crystal and molecular structure of amidopyrine

Amidopyrine (1-phenyl-2,3-dimethyl-4-dimethylaminopyrazolone), C13HzvN30, a dimethylamino derivative of antipyrine and an important analgesic and antipyretic agent, crystallizes in the triclinic space group P1 with four molecules in a unit cell of dimensions a= 7.458 (5), b = 10.744 (5), c= 17.486 (15)/~,, e=98.6 (2),/~= 85.6 (3), y= 108-6 (2) . The structure was solved by direct methods and refined to an R value of 0.055 for 3706 photographically observed reflexions. The dimensions of the two crystallographically independent molecules are very nearly the same. The pyrazolone moiety in the molecule has dimensions comparable to those in antipyrine. Unlike antipyrine, the molecular dimensions of amidopyrine in the free state (the present structure) are close to those found in some of its hydrogenbonded complexes. Thus it appears that the presence of the dimethylamino group makes the molecule more resistant to changes in its dimensions resulting from molecular association. An attempt has also been made to correlate the polar nature of the pyrazolone moiety and the hybridization state of the hetero nitrogen atoms in antipyrine, amidopyrine and their complexes.

The Crystal and Molecular Structure of 4-Aza-5-oxo-tricyclo[4.4.0.03,8]decane (Aza-twistanone)

Die kristalline Struktur von Aza-twistanon wurde durch eine Röntgenstruktur-analyse untersucht. Die Kristalle gehören zur monoklinen Raumgruppe P21/n mit den Zelldimensionen a = 6,662(6), b = 13,36(2), c = 8,606(9) Å, = 98,97(2)°, V = 757 Å3, Z = 4. Die Struktur wurde mit Direktmethoden gelöst und bis zu R = 0,035 verfeinert (mittlere (c) = 0,003 Å3).Die cis-Amidgruppe ist relativ stark deformiert und hat einen Torsionswinkel C -C -N-C von 14,5(4)° (Deformation aus der Ebene c = 5,0(5)° und N = 13,5(4,0)°). Die gegenüberliegende äthylenbrücke weist einen Torsionswinkel von 25,1(5)° auf. Die entsprechenden Winkel in Twistan betragen je 20°. Das tricyclische Gerüst von Aza-twistanon hat approximative.