Conformational characteristics of the hexanucleoside pentaphosphate AUAUAU: a 2D NMR study at 500 MHz.

All 36 ribose proton resonances and most of the base proton resonances of the hexanucleoside pentaphosphate AUAUAU have been assigned unequivocally using 2D J-resolved spectroscopy, spin echo correlated spectroscopy (SECSY) and 2D NOE spectroscopy (NOESY). The NMR parameters of AUAUAU are compared with those of smaller fragments that contain methylated adenine bases: m62AU, m62AUm62A, m62AUm62AU and m62AUm62AUm62A. Previous studies on this series of compounds have shown that in all these cases purine-pyrimidine-purine sequences prefer to adopt a mixture of states which have as common feature that the interior pyrimidine residues are bulged out, whereas the purine residues stack upon each other. Chemical shift data, proton-proton coupling constants, as well as the observation of imino-proton resonances for AUAUAU show unambiguously that upon lowering the temperature the high-temperature "bulged out" situation reverts to a normal A-RNA-like double helix.     

Carbon-13 NMR in conformational analysis of nucleic acid fragments. Heteronuclear chemical shift correlation spectroscopy of RNA constituents.

The assignment of the non-quaternary 13C resonances by means of two-dimensional heteronuclear chemical shift correlation spectroscopy is presented for several oligoribonucleotides: The dimers m6(2)AU, m6(2)Am6(2)A and mpUm6(2)A and the trimers m6(2)AUm6(2)A and m4(2)Cm4(2)Cm6(2)A. The temperature and concentration dependency of the 13C chemical shifts are studied with emphasis on the behaviour of the dimer m6(2)AU. The present study shows that in the 5-50 mM range the concentration-dependent chemical shift changes of the ribose carbons are negligible compared to chemical shift changes due to intramolecular events. All compounds studied show a surprising correlation between the chemical shifts of the carbon atoms of the ribose ring and the sugar conformational equilibrium as expressed by the percentage N or S conformer. Thus the chemical shift data can be used to obtain the thermodynamical parameters of the two-state N/S equilibrium. Parameters deduced for m6(2)AU are Tm = 306 K and delta S = -25 cal mol-1 K-1, which values are in satisfactory agreement with results obtained earlier from 1H NMR and from Circular Dichroism.     

Influence of uracil on the conformational behaviour of RNA oligonucleotides in solution

NMR studies were carried out on some alternating pyrimidine-purine sequences: the single-stranded tetramers CACA and UGUG and the self-complementary octamer CACAUGUG. Assignments, based upon COSY, homonuclear Hartmann-Hahn, and NOESY experiments, are given for the resonances of all base protons and of several sugar protons. Chemical shift vs temperature profiles were used to obtain thermodynamic parameters for the single-stranded stack in equilibrium with random coil and the duplex in equilibrium with random coil equilibria. The populations of N-type conformer of the ribose rings were estimated from the observed J1'2'. Comparisons with another alternating pyrimidine-purine sequence Um2(6)AUm2(6)A and with the deoxyribose counterparts d(CACA), d(TGTG) and d(CACATGTG) are given. Previous 1H-NMR investigations of Um2(6)AUm2(6)A revealed that the population of bulge-out structure diminishes compared to m2(6)AUm2(6)A due to the U(1)-m2(6)A(2) stacking interaction. In CACA a strong stacking proclivity (Tm = 310 K) together with a clear preference for N-type ribose is observed. However, the stacking interactions in UGUG are relatively less stable (Tm = 288 K) and a bias towards S-type sugar is present. Besides a small amount of stack, a significant contribution of bulge out structure is proposed for UGUG. We conclude that the nature of the pyrimidine base mainly determines the formation of bulge-out structures. The poor stacking properties of uracil now appear to be mainly responsible for this phenomenon. Comparison with the deoxyribose counterparts shows a reasonable agreement between the Tm values of CACA and d(CACA), whereas the Tm of UGUG (288 K) is much lower than the Tm of d(TGTG) (315 K). It is suggested that the absence of bulge-out structures in DNA purine-pyrimidine-purine sequences is related to the relatively strong stacking proclivity of dT residues compared to that of U residues. The Tm values (average 341 K) for the duplex in equilibrium with random coil transition obtained for each residue of CACAUGUG appear very similar. All ribose rings, except the G(8), adopt a pure N conformer in the duplex. This is taken to mean that the differences in conformational behaviour of the constituent tetramers disappear upon duplex formation.     

Transparent cellulose films with high gas barrier properties fabricated from aqueous alkali/urea solutions

Transparent and bendable regenerated cellulose films prepared from aqueous alkali (NaOH or LiOH)/urea (AU) solutions exhibit high oxygen barrier properties, which are superior to those of conventional cellophane, poly(vinylidene chloride), and poly(vinyl alcohol). Series of AU cellulose films are prepared from different cellulose sources (cotton linters, microcrystalline cellulose powder, and softwood bleached kraft pulp) for different dissolution and regeneration conditions. The oxygen permeabilities of these AU cellulose films vary widely from 0.003 to 0.03 mL μm m(-2) day(-1) kPa(-1) at 0% relative humidity depending on the conditions used to prepare the films. The lowest oxygen permeability is achieved for the AU film prepared from 6 wt % cellulose solution by regeneration with acetone at 0 °C. The oxygen permeabilities of the AU cellulose films are negatively correlated with their densities, and AU films prepared from solutions with high cellulose concentrations by regeneration in a solvent at low temperatures generally have low oxygen permeabilities. The AU cellulose films are, therefore, promising biobased packaging materials with high-oxygen barrier properties.     

Binuclear platinum (II)-terpyridine complexes. A new class of bifunctional DNA-intercalating agent.

A series of binuclear DNA-binding ligands was prepared by linking two (2,2':6',2"-terpyridine)platinum(II) moieties via alpha omega-dithiols of the type HS-[CH2]n-SH where n = 4-10. A monomeric analogue was also synthesized. Compounds were characterized by elemental analysis and electronic and n.m.r. spectroscopy. Viscometric measurements with sonicated rod-like DNA fragments and covalently closed circular DNA were performed to investigate the mode of binding of these agents. The ligands with n = 5 and 6 function as bis intercalators and form a single 'base-pair sandwich' in violation of neighbour-exclusion binding. Bifunctional reaction occurs for the ligand with n = 7, whereas the ligands with n = 8 and 10 show a preference for mixed monofunctional/bifunctional binding. The data do not permit definitive assignment of the binding mode of the ligands with n = 4 and 9. All compounds are growth-inhibitory against mouse leukaemia L1210 cells in culture with IC50 values in the range 2-14 microM.     

The preferred conformations of protected homodito homoheptamethionine peptides. A1 H n.m.r. study in deuterochloroform medium

Detailed analyses of the conformations of the homo-oligopeptide series, Boc-(L-Met)n-OME n = 2--7, in deuterochloroform have been carried out with proton n.m.r. and IR spectroscopy. Well-resolved high field n.m.r. spectra with assignments for the NH and alpha-CH resonances of these homo-methionine peptides are presented. Extensive n.m.r. concentration-dependent chemical shift studies are combined with IR results to delineate the involvement of the various methionine NH protons in intra- and/or intermolecular hydrogen bonding. N.m.r. chemical shift dependencies with temperature and solvent, DMSO-d6, are used to explore the strength of the hydrogen bonds for the various oligopeptides. At low concentrations, where peptide aggregation is absent, the dipeptide is found to be disordered. The tetra- to heptapeptides possess intramolecular hydrogen bonded seven-membered rings at internal residues. The number of internal rings and the oligopeptide self-association increase with increasing peptide chainlength. At intermediate concentrations associations of peptide molecules with folded structures occur with initial association at the C-terminal region. At high concentrations, "in-register" associated extended beta structures are formed.     

Photodynamic and peptide-based strategy to inhibit Gram-positive bacterial biofilm formation

Abstract

The self-produced extracellular polymeric matrix of biofilms renders them difficult to eliminate once they are established. This makes the inhibition of biofilm formation key to successful treatment of biofilm infection. Antimicrobial photodynamic therapy (aPDT) and antimicrobial peptides offer a new approach as antibiofilm strategies. In this study sub-lethal doses of aPDT (with chlorin-e6 (Ce6-PDT) or methylene blue (MB-PDT)) and the peptides AU (aurein 1.2 monomer) or (AU)₂K (aurein 1.2?C-terminal dimer) were combined to evaluate their ability to prevent biofilm development by Enterococcus faecalis. Biofilm formation was assessed by resazurin reduction, confocal microscopy, and infrared spectroscopy. All treatments successfully prevented biofilm development. The (AU)₂K dimer had a stronger effect, both alone and combined with aPDT, while the monomer AU had significant activity when combined with Ce6-PDT. Additionally, it is shown that the peptides bind to the lipoteichoic acid of the E. faecalis cell wall, pointing to a possible key mechanism of biofilm inhibition.     

Homologous RNA recombination in brome mosaic virus: AU-rich sequences decrease the accuracy of crossovers.

Brome mosaic virus, a tripartite positive-stranded RNA virus of plants, was used for the determination of sequence requirements of imprecise (aberrant) homologous recombination. A 23-nucleotide (nt) region that included a 6-nt UUAAAA sequence (designated the AU sequence) common between wild-type RNA2 and mutant RNA3 supported both precise and imprecise homologous recombination, though the latter occurred with lower frequency. Doubling the length of the 6-nt AU sequence in RNA3 increased the incidence of imprecise crossovers by nearly threefold. Duplication or triplication of the length of the AU sequence in both RNA2 and RNA3 further raised the frequency of imprecise crossovers. The majority of imprecise crosses were located within or close to the extended AU sequence. Imprecise recombinants contained either nucleotide substitutions, nontemplated nucleotides, small deletions, or small sequence duplications within the region of crossovers. Deletion of the AU sequence from the homologous region in RNA3 resulted in the accumulation of only precise homologous recombinants. Our results provide experimental evidence that AU sequences can facilitate the formation of imprecise homologous recombinants. The generation of small additions or deletions can be explained by a misannealing mechanism within the AU sequences, while replicase errors during RNA copying might explain the occurrence of nucleotide substitutions or nontemplated nucleotides.     

Conformational analysis of a modified ribotetranucleoside triphosphate: m6(2)A-U-m6(2)A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz

The complete and unequivocal assignment of the 24 ribose proton signals of m6(2)A(1)-U(2)-m6(2)(3)-U(4) by means of 500 MHz NMR spectroscopy at 17 degrees C is given. this assignment is based on scrupulous decoupling experiments carries out at various temperatures. Analysis of the observed chemical shifts and coupling constants of the tetramer shows that the two fragments -m6(2)A(3)-U(4) comprising the 3'-end occur mainly in the classical right-handed stack conformation, whereas the 5'-end the -U(2)- residue appears bulged out in favour of a less well-defined stacking interaction between the bases m6(2)A(1)-and -m6(2)A(3)-. Conformational populations about each of the torsional degrees of freedom along the backbone are discussed. A modernized version of pseudorotation analysis is used to delineate the conformational behaviour of the four ribose rings.     

EPR spectroscopic detection of free radical outflow from an isolated muscle bed in exercising humans.

There is no direct evidence to support the contention that contracting skeletal muscle and/or associated vasculature generates free radicals in exercising humans. The unique combination of isolated quadriceps exercise and the measurement of femoral arterial and venous free radical concentrations with the use of electron paramagnetic resonance (EPR) spectroscopy enabled this assumption to be tested in seven healthy men. Application of ex vivo spin trapping using alpha-phenyl-tert-butylnitrone (PBN) resulted in the detection of oxygen- or carbon-centered free radicals (a(N) = 1.38 +/- 0.01 mT and a(beta)(H) = 0.17 +/-0.01 mT, where a(N) and a(beta)(H) are the nitrogen and beta-hydrogen coupling constants, respectively) with consistently higher EPR signal intensities of the PBN spin adduct observed in the venous compared with the arterial circulation (P < 0.05). Incremental exercise further increased the venoarterial intensity difference [85 +/- 58 arbitrary units (AU) at 24 +/- 6% maximal work rate (WR(max)) vs. 387 +/- 214 AU at 69 +/- 7% WR(max); P < 0.05]. When combined with measured changes in femoral venous blood flow (Q), this resulted in a net adduct outflow of 130 +/- 118 and 1,146 +/- 582 AU/min (P < 0.05), which was positively associated with leg oxygen uptake (r(2) = 0.47, P < 0.05) and Q (r(2) = 0.47, P < 0.05). These results provide the first evidence for oxygen- or carbon-centered free radical outflow from an active muscle bed in humans.     

两种过路黄的核型研究

对国产报春花科珍珠菜属植物过路黄和疏节过路黄的核型进行了首次报道。过路黄染色体数目为２ｎ＝２４,核型公式为２ｎ＝２４＝２ｍ＋４ｓｍ＋６ｓｔ＋１２ｔ,核型类型“３Ａ”;疏节过路黄染色体数目为２ｎ＝２２,核型公式为２ｎ＝２２＝４ｍ＋６ｓｍ＋１０ｔ,核型类型“３Ａ”。     

Structural features of a water-soluble arabinoxylan from the endosperm of wheat.

A cold-water-soluble wheat-endosperm arabinoxylan consisting of a backbone of (1----4)-linked beta-D-xylopyranosyl residues that are variously unsubstituted, and 3- or 2,3-substituted with single alpha-L-arabinofuranosyl groups, was subjected to 1H-n.m.r. spectroscopy. The results of 2D homonuclear Hartmann-Hahn and 1D 1H-n.m.r. spectroscopy allowed the identification of 3- and 2,3-substituted xylose residues, each with adjacent unsubstituted xylose residues, and also substituted xylose residues with a substituted xylose residue as a neighbour. The 1H-n.m.r. data were correlated with 13C-n.m.r. data by means of a 13C-1H 2D proton-detected heteronuclear multiple-quantum correlation experiment, which showed that only different types of branching (i.e., 3- and 2,3-) can be identified by the 13C-n.m.r. data.     

两种过路黄的核型研究

对国产报春花科（Ｐｒｉｍｕｌａｃｅａｅ）珍珠菜属（Ｌｙｓｉｍａｃｈｉａ）植物过路黄（Ｌ.ｃｈｒｉｓｔｉｎａｅＨａｎｃｅ）和疏节过路黄（Ｌ.ｒｅｍｏｔａＰｅｔｉｔｍ）的核型进行了首次报道。过路黄染色体数目为２ｎ＝２４,核型公式为２ｎ＝２４＝２ｍ＋４ｓｍ＋６ｓｔ＋１２ｔ,核型类型“３Ａ”;疏节过路黄染色体数目为２ｎ＝２２,核型公式为２ｎ＝２２＝４ｍ＋６ｓｍ＋２ｓｔ＋１０ｔ,核型类型“３Ａ”。     

Effect of amino substitution on the excited state dynamics of uracil.

The excited state deactivation of two amino-substituted uracils, 5-aminouracil (5AU) and 6-aminouracil (6AU) in aqueous solution was studied by femtosecond fluorescence upconversion. The fluorescence of 6AU decays as fast as that of uracil with a unique time constant of about 100 femtoseconds. The fluorescence of 5AU exhibits a more complex behavior, fundamentally different from what we found in any other uracils: the decays are globally slower (up to several picoseconds) and depend strongly on the wavelength. This difference is attributed to the particular character of the amino group, affecting the out-of-plane motion of the 5-substituent which has been shown to be crucial for the ultrafast internal conversion occurring in uracils. Our observations indicate instead the formation of a transient fluorescent state which in turn is deactivated by a different relaxation process specific to the amino group.     

Complete 1H- and 13C-n.m.r. assignments for two sulphated oligosaccharide alditols of hen ovomucin

The complete 1H- and 13C-n.m.r. assignments for beta-D-Galp-(1----4)-beta-D-GlcpNAc-6-SO3H-(1----6)-[beta-D-Galp-(1----3 )]- D-GalNAcol and alpha-NeuAcp-(2----3)-beta-D-Galp-(1----3)-[beta-D-Galp-(1----4)-b eta-D- GlcpNAc-6-SO3H-(1----6)]-D-GalNAcol were made by a combination of 2-D correlation experiments (Relayed-Cosy; and 13C,1H Correlation-shift n.m.r. spectroscopy), and 1-D n.m.r. spectroscopy. The results illustrate the ability of these methods to locate sulphate and NeuAc groups in anionic mucinous glycoproteins.     

豆科山羊豆族2属5种植物的核型分析

报道了产于中国西北地区豆科山羊豆族2属5种植物的核型.结果表明,这5种豆科植物均为二倍体,其核型公式分别为:单叶黄耆(Astragalus efoliolatus),2n=16=12m 4sm,2A"核型;鸡峰山黄耆(A.kifonsanicus),2n=16=12m 4sm,2A"核型;太原黄耆(A.taiyuanensis),2n=16=8m 6sm 2t(2SAT),2B"核型;变异黄耆(A.variabilis),2n=16=14sm 2t(2SAT),3A"核型;贺兰山岩黄耆(Hedysarum petrovii),2n=16=12m 4sm(2SAT),2A"核型.除变异黄芪外,其余各种的染色体数目及核型均为首次报道.     

中国西北地区11种黄耆属植物的细胞学研究

对分布于中国西北地区的11种黄耆属植物进行了细胞学研究,其中9种作了核型分析。结果表明,杯萼黄耆（Astragalus cupulicalycinus）为六倍体（2n=48）,酒泉黄耆（A.jiuquanensis）具有2种细胞型：2n=32的四倍体和2n=48的六倍体,其余种类均为二倍体（2n=16)。9个种的核型公式分别为：木黄耆（A.arbuscula）,2n=16=14 2sm,“1A”核型;胀萼黄耆（A.ellipsoideus）,2n=16=10m 6sm,“2A”核型;粗毛黄耆（A.scabrisetus),2n=16=14m 2sm,“1A”核型;秦岭黄耆（A.henryi),2n=16=8m 8sm(2SAT),“2A”核型;哈巴河黄耆（A.habaheensis）,2n=16=10m 6sm(2SAT),“2A”核型;变异黄耆（A.variabilis）,2n=16=4m 10sm(2SAT) 2t,“2A”核型;喜沙黄耆（A.ammodytes),2n=16=6m 10sm(2SAT),“2A”核型;密花黄耆（A.densiflorus),2n=16=6m(2SAT) 10sm,“2A”核型;茧荚黄耆（A.lehmannianus),2n=16=14m(2SAT) 2st,“2A”核型。所有研究种中,仅变异黄耆的染色体数目有过报道,其余种的染色体数目及核型均为首次报道。     

Systematic comparisons of artificial urine formulas for in vitro cellular study

Artificial urine (AU) is widely used for in vitro cellular study to simulate normal physiological environment of the kidney and urinary tract. However, some compositions of many of previously established AU formulas are out of their physiological ranges in normal human urine. Therefore, we established a new AU formula, named “AU-Siriraj,” and then performed systematic comparisons of AU-Siriraj with other six previously established AU formulas, ultrafiltrated (UF) urine, and blank-control to determine their compatibility with MDCK cells. The data indicate that AU-Siriraj is the best, and AU-3 is the second best, AU formula for in vitro cellular study.     

Conformation and dynamics of the deoxyribose rings of a (nogalamycin)2-d (5''-GCATGC)2 complex studied in solution by 1H-n.m.r. spectroscopy.

The conformation and dynamics of the deoxyribose rings of a (nogalamycin)2-d(5'-GCATGC)2 complex have been determined from an analysis of 1H-1H vicinal coupling constants and sums of coupling constants (J1'-2',J1'-2",epsilon 1', epsilon 2' and epsilon 2") measured from one-dimensional n.m.r. spectra and from H-1'-H-2' and H-1'-H-2" cross-peaks in high-resolution phase-sensitive two-dimensional correlation spectroscopy (COSY) and double-quantum-filtered correlation spectroscopy (DQF-COSY) experiments. The value of J3'-4' has also been estimated from the magnitude of H-3'-H-4' cross-peaks in DQF-COSY spectra and H-1'-H-4' coherence transfer cross-peaks in two-dimensional homonuclear Hartman-Hahn spectroscopy (HOHAHA) spectra. The data were analysed, in terms of a dynamic equilibrium between North (C-3'-endo) and South (C-2'-endo) conformers, by using the graphical-analysis methods described by Rinkel & Altona [(1987) J. Biomol. Struct. Dyn. 4,621-649]. The data reveal that the sugars of the 2C-5G and 3A-4T base-pairs, which form the drug-intercalation site, have strikingly different properties. The deoxyribose rings of the 2C-5G base-pair are best described in terms of an equilibrium heavily weighted in favour of the C-2'-endo geometry (greater than 95% 'S'), with a phase angle, P, lying in the range 170-175 degrees and amplitude of pucker between 35 and 40 degrees, as typically found for B-DNA. For the deoxyribose rings of the 3A-4T base-pair, however, the analysis shows that, for 3A, the C-2'-endo and C3'-endo conformers are equally populated, whereas a more limited data set for the 4T nucleotide restricts the equilibrium to within 65-75% C-2'-endo. The deoxyribose rings of the 1G-6C base-pair have populations of 70-80% C-2'-endo, typical of nucleotides at the ends of a duplex. Although drug-base-pair stacking interactions are an important determinant of the enhanced duplex stability of the complex [Searle, Hall, Denny, & Wakelin (1988) Biochemistry 27, 4340-4349], the current findings make it clear that the same interactions can be associated with considerable variations in the degree of local structural dynamics at the level of the sugar puckers.