Hydrogen bonding in nucleosides and nucleotides

An analysis of the hydrogen bonding in 76 nucleoside and 11 nucleotide crystal structures shows that the hydrogen bond lengths fall into well-defined categories according to the nature of the donor or acceptor groups. The shortest bonds are those involving P---OH or O=P groups. For donor groups, the sequence in bond lengths is

P—OH<C—OH< N−H<O_w(H)—H<N(H)—H<C−H

There are ten examples of two centre

H—H…O

bonds, which are comparable in length with P---OH …O bonds. The acceptor seqeunce is

O=P<OH₂<OH₂<O=CO(H)C<N N(H₂)C<Cl^…<O<S=C

The number of three-centre bonds, about 24%, is comparable to that observed in the carbohydrates and the amino acids. Most hydrogen bonds are involved in short finite chains. Only in the nucleotides are cyclic hydrogen bonding schemes observed.     

Oxidation of 1,4-alkanediols into γ-lactones via γ-lactols using Rhodococcus erythropolis as biocatalyst

Whole cells of Rhodococcus erythropolis DSM 44534 grown on ethanol, (R)- and (S)-1,2-propanediol were used for biotransformation of racemic 1,4-alkanediols into γ-lactones. The cells oxidized 1,4-decanediol (1a) and 1,4-nonanediol (2a) into the corresponding γ-lactones 5-hexyl-dihydro-2(3H)-furanone (γ-decalactone, 1c) and 5-pentyl-dihydro-2(3H)-furanone (γ-nonalactone, 2c), respectively, with an EE(R) of 40–75%. The transient formation of the γ-lactols 5-hexyl-tetrahydro-2-furanol (γ-decalactol, 1b) and 5-pentyl-tetrahydro-2-furanol (γ-nonalactol, 2b) as intermediates was observed by GC–MS. 1,4-Pentanediol (3a) was transformed into 5-methyl-dihydro-2(3H)-furanone (γ-valerolactone, 3c) whereas (R)- and (S)-2-methyl-1,4-butanediol (4a) was converted to the methyl-substituted γ-butyrolactones 4-methyl-dihydro-2(3H)-furanone (4c₁) and 3-methyl-dihydro-2(3H)-furanone (4c₂) in a ratio of 80:20 with a yield of 55%. Also cis-2-buten-1,4-diol (5a) was transformed resulting in the formation of 2(5H)-furanone (γ-crotonolactone, 5c). At the higher pH values of 8.8 the yield of lactone formed was improved; however, the enatiomeric excesses were slightly higher at the lower pH of 5.2.     

84K杨PagC3H3基因表达模式分析

木质素作为木材的主要组成成分,通常是由3种单体聚合而成,在其生物合成过程中,共有10个酶家族参与负责将苯丙胺酸转化为单体木质素,其中C3H是在对-香豆酰辅酶A（p-coumaroyl CoA）到咖啡酰辅酶A（caffeoyl CoA）的羟基化过程和G/S单体形成中的关键控制酶类,探究PagC3H3基因表达模式,对于进一步了解该基因功能具有重要意义。该研究通过定量PCR对PagC3H3基因的组织特异性表达进行分析;克隆得到了长度为2 035 bp的PagC3H3的启动子序列,预测含有多个顺式作用元件;同时,将获得的PagC3H3的启动子序列构建植物表达载体pBI121-PagC3H3pro：：GUS,进行拟南芥瞬时转化,结果显示PagC3H3基因在84K杨的根、中部茎节和基部茎节中的表达量较高;瞬时转化拟南芥,GUS染色表明：在下胚轴和根中GUS活性较强,由此推测PagC3H3基因在木质素合成过程中发挥作用。     

Determination of free energies in reaction centers of Rb. sphaeroides

Magnetic field-dependent recombination measurements together with magnetic field-dependent triplet lifetimes (Chidsey, E.D., Takiff, L., Goldstein, R.A. and Boxer, S.G. (1985) Proc. Natl. Acad. Sci USA 82, 6850–6854) yield a free energy change ΔG(P⁺H⁻ − ³P*) = 0.165 eV ±0.008 at 290 K. This does not depend on whether nuclear spin relaxation in the state ³P* is assumed to be fast or slow compared to the lifetime of this state. This value, being (almost) temperature independent, indicates ΔG(P⁺H⁻ − ³P*) ΔH(P⁺H⁻ − ³P*) and is consistent with ΔG(¹P* − P⁺H⁻) and ΔH(¹P* − ³P*) from previous delayed fluorescence and phosphorescence data, implying ΔG ΔH for all combinations of these states.     

P-3A and (−)-desacetamido P-3A: demonstration and Study of their effective functional cleavage of duplex DNA

A study of the Fe(II) complexes of P-3A (1) and (−)-desacetamido P-3A (2) abilities to cleave duplex DNA was conducted through examination of single-strand and double-strand cleavage of supercoiled φX174 RFI DNA (Form I) in the presence of O₂ to produce relaxed (Form II) and linear (Form III) DNA, respectively. Like Fe(II)-bleomycin A₂ and deglycobleomycin A₂, Fe(II)-1 and 2 effectively produced both single- and double-strand cleavage of supercoiled φX174 DNA. Unlike Fe(II)-bleomycin A₂ or deglycobleomycin A₂, Fe(II)-1 and 2 were found to cleave duplex w794 DNA with no discemible sequence selectively suggesting that the polynucleotide recognition of the C-terminus tetrapeptide S subunit of the bleomycins including the bithiazole may dominate the bleomycin A₂ DNA cleavage selectivity.     

Synthesis and anticancer evaluation of certain indolo[2,3-b]quinoline derivatives

The present report describes the synthesis and anticancer evaluation of certain 11-substituted 6H-indolo[2,3-b]quinolines and their methylated derivatives. These 6H-indolo[2,3-b]quinoline derivatives 11–13 were prepared from the commercially available 1,4-dihydroxyquinoline through alkylation, chlorination, nucleophilic reaction, and ring cyclization. Depending on the ratio of 11, (MeO)₂SO₂, and K₂CO₃, alkylation occurred primarily on N-5 (1:0.8:0.8) or N-6 (1:1.5:1.5) leading to the isolation of 14a or 14b as a major product. Accordingly, major product 15a (2/(MeO)₂SO₂/K₂CO₃ = 1:2:2) or 15b (1:1:1), respectively, was obtained by alkylation of 12 while 16a (13/(MeO)₂SO₂/K₂CO₃ = 1:2:2) or 16b (1:1:1), respectively, was obtained by alkylation of 13. The in vitro anticancer assay indicated 5-methylated derivatives 14a, 15a, 16a are more cytotoxic than their respective 6-methylated counterparts 14b, 15b, 16b and 6H-indolo[2,3-b]quinoline precursors 11, 12, 13. Among them, 11-(4-methoxyanilino)-6-methyl-6H-indolo[2,3-b]quinoline (16a) was the most cytotoxic with a mean GI₅₀ value of 0.78 μM and also exhibited selective cytotoxicities for HL-60 (TB), K-562, MOLT-4, RPMI-8226, and SR with GI₅₀ values of 0.11, 0.42, 0.09, 0.14, and 0.19 μM, respectively.     

A pterocarpan and two isoflavans from alfalfa

(−)6aR,11aR-Dihydro-3-hydroxy-9,10-dimethoxy-6H-benzofuro[3,2c] [1]-benzopyran (10-methoxymedicarpin), (+)-(2,3,4,-trimethoxyphenyl)-2,3-dihydro-7-hydroxy-4H-1-benzopyran (7-hydroxy-2′,3′,4′-trimethoxyisoflavan) and (+)-(2,3,4-trimethoxy-5-hydroxyphenyl)-2,3-dihydro-7-hydroxy-4H-1-benzopyran (7,5′-dihydroxy-2′,3′,4′-trimethoxyisoflavan) were isolated for the first time from dried Medicago sativa hay. Structural assignments were based on ¹H NMR and mass spectra, X-ray crystallography, and optical rotations.     

Genetic control of the UV-induced SOS mutator effect in single- and double-stranded DNA phages

The SOS hypothesis postulated that the mutator effect on undameged DNA that generates phage-untargeted mutagenesis (UTM) results directly from the mechanism of targeted mutagenesis. RecA protein, which stimulates the cleavage of both the LexA repressor and UmuD protein, and the UmuDC gene products are required for UV-induced targeted mutagenesis. The use of phage λ for analyzing UV-induced mutagenesis has permitted a distinction to be made between the mechanisms of targeted and untargeted mutagenesis, in that the two processes differ with respect to their genetic requirements for recA⁺ and umuDC⁺ genes. In this paper, we show thet (i) proficiency for excision repair is required for UTM in double-stranded DNA phage but not in single-stranded DNA phage; (ii) the umuC function, which is not required for UTM of the double-stranded DNA phage λ, is necessary for untargeted mutagenesis of the single-stranded DNA phages M13 and φX174; (iii) for both single-stranded and double-stranded DNA phage, UV irradiation of the host increases the level of recA730-induced UTM. Our results are also consistent with the interpretation that the expression of untargeted mutagenesis in phage λ and in M13 depends on the polymerase and to a lesser extent on the exonuclease 5′ → 3′, activities of Po1I. These results suggest that the involvement of the RecA and UmuDC proteins may be related to more than the presence of base damage in the DNA substrate.     

Variation in δC values for the seagrass Thalassia testudinum and its relations to mangrove carbon

Carbon isotope ratios (¹³C/¹²C) were measured for the leaves of the seagrass Thalassia testudinum Banks ex König and carbonates of shells collected at the seagrass beds from seven sites along the coast of southern Florida, U.S.A. The δ¹³C values of seagrass leaves ranged from −7.3 to −16.3‰ among different study sites, with a significantly lower mean value for seagrass leaves from those sites near mangrove forests (−12.8 ± 1.1‰) than those far from mangrove forests (−8.3 ± 0.9‰; P < 0.05). Furthermore, seagrass leaves from a shallow water area had significantly lower δ¹³C values than those found in a deep water area (P < 0.01). There was no significant variation in δ¹³C values between young and mature leaves (P = 0.59) or between the tip and base of a leaf blade (P = 0.46). Carbonates of shells also showed a significantly lower mean δ¹³C value in the mangrove areas (−2.3 ± 0.6‰) than in the non-mangrove areas (0.6 ± 0.3‰; P <0.025). In addition, the δ¹³C values of seagrass leaves were significantly correlated with those of shell carbonates (δ¹³C seagrass leaf = −9.1 + 1.3δ¹³C shell carbonate (R² = 0.83, P < 0.01)). These results indicated that the input of carbon dioxide from the mineralization of mangrove detritus caused the variation in carbon isotope ratios of seagrass leaves among different sites in this study.     

Plant nutrient dynamics and stoichiometric homeostasis of invasive species Spartina alterniflora and native Cyperus malaccensis var. brevifolius in the Minjiang River estuarine wetlands

Aims Stoichiometric homeostasis is an important mechanism in maintaining ecosystem structure, function, and stability. The invasion of exotic species, Spartina alterniflora, has largely threatened the structure and function of native ecosystems in the Minjiang River estuarine wetland. However, how S. alterniflora invasion affect plant stoichiometric homeostasis is largely unknown. This could enhance our understanding on wetland ecosystem stability and expand the applications of ecological stoichiometry theory.
Methods Nitrogen (N) and phosphorus (P) contents of plant organs and soils in the S. alterniflora, Cyperus malaccensis var. brevifolius, and S. alterniflora-C. malaccensis var. brevifolius mixture were measured, and the homeostatic index (H) was calculated according to the stoichiometric homeostasis theory.
Important findings Our results showed that the invasion of S. alterniflora significantly increased soil N:P ratio (p < 0.05), but did not affect soil N or P contents. The N and P contents of leaf and stem were the highest for S. alterniflora, and those of the stem were the highest for C. malaccensis var. brevifolius. At the ecosystem level, the average of homeostatic index (H) of N (H_N, 25.31) was larger than those of P (H_P, 10.33) and N:P (H_N:P, 2.50). At the organ level, root H_N was significantly larger than stem H_N (p < 0.05) and sheath H_N:P was greater than root H_N:P (p < 0.05), while there was no significant difference for H_P among root, stem, leaf, and sheath (p > 0.05). As for species, root H_N of S. alterniflora was significantly larger than that of C. malaccensis var. brevifolius in the mixture community (p < 0.05). In the monoculture, stem H_N:P of S. alterniflora was significantly higher than that of C. malaccensis var. brevifolius (p < 0.05). Furthermore, root H_N, leaf H_N and sheath H_N of S. alterniflora in the mixed community was significantly larger than that of S. alterniflora in the monoculture (p < 0.05), suggesting that S. alterniflora invasions increased their stoichiometric homeostasis. Meanwhile, the stoichiometric homeostasis of invasive and native plants were influenced by multiple factors, such as nutrients, organs, vegetation, and invasion. However, larger homeostasis was found in S. alterniflora than in C. malaccensis var. brevifolius in some particular organs either in mixture or monoculture communities. Therefore, the successful invasion of S. alterniflora may result from higher homeostatic index than the native species, C. malaccensis var. brevifolius.     

Iron-chlorophyllin-mediated conversion of 3-hydroxyamino-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2(NHOH)) into its nitroso derivative

Early work from our laboratory has shown that the mutagenicity of heterocyclic amines in Salmonella can be inhibited by hemin and chlorophyllins. We have speculated that the inhibition is a result of complex formation between heterocyclic amines and the pigments, and the speculation has been given a line of experimental evidence. We have now found that ferric-chlorophyllin (Fe-chlorophyllin) can modify the mutagenicity of 3-hydroxyamino-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2(NHOH)), a metabolically activated form of 3-amino-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2). The mutagenicity of Trp-P-2(NHOH)) in Salmonella typhimurium TA 98 (without S9) was strongly inhibited by an addition of an equimolar Fe-chlorophyllin in the pre-incubation mixture. Fe-chlorophyllin also inhibited the mutagenicity of 2-hydroxyamino-6-methyldipyrido[1,2-a:3′,2′-d] imidazole (Glu-P-1(NHOH)). A rapid change in the UV spectrum of a mixture of Trp-P-2(NHOH) and Fe-chlorophyllin was observed. Analysis by high performance liquid chromatography showed that Trp-P-2(NHOH) was converted into 3-nitroso-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2(NO)), the mutagenic potency of which is a quarter of that of Trp-P-2(NHOH). Furthermore, the mutagenicity of Trp-P-2(NO), in turn, was inhibited by Fe-chlorophyllin. We conclude that the suppression of the mutagenicity of Trp-P-2(NHOH) is ascribable to the oxidative function of Fe-chlorophyllin, coupled with its ability to form complex formation with the planar surface of the heterocyclic amine molecules.     

Evidence for Ca-dependent protein phosphorylation in vitro in guard cells from Vicia faba L.

Protein phosphorylation in vitro was investigated in guard cells from Vicia faba. A number of proteins with apparent molecular masses of 72, 67, 57, 52, 49, 44, 37, and 26 kDa were phosphorylated when guard-cell extract was incubated with [γ-³²P]ATP under Ca²⁺-free conditions. In the presence of Ca²⁺ at 1 μM, several proteins with apparent molecular masses of 125, 83, 41, 31, and 25 kDa were newly phosphorylated. These Ca²⁺-dependent protein phosphorylations were suppressed by (8R^*,9S^*,11S^*)-(−)-9-hydroxy-9-methoxycarbonyl-8-methyl-2,3,9,10-tetrahydro-8,11-epoxy-1H,8H,11H-2,7b,11a- triazadibenzo[a,g]cycloocta[cde]trinden-1-one (K-252a), a wide-range inhibitor of protein kinases, suggesting that the protein phosphorylations were mediated by protein kinases. Several proteins were phosphorylated in vitro in mesophyll extract from Vicia. In contrast to guard cells, there was no detectable Ca²⁺-dependent protein phosphorylation in mesophyll cells. 1-(5-Indonaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine (ML-7), an inhibitor of myosin light chain kinase (MLCK), and an antagonist of calmodulin (CaM), N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), inhibited Ca²⁺-dependent phosphorylation of 41- and 25-kDa proteins in guard cells. Fractionation experiments revealed that the Ca²⁺-dependent phosphorylated proteins with molecular masses of 41 and 25 kDa were present in the mitochondria, and the 125- and 31-kDa proteins in the cytosol. These results suggest that Ca²⁺-dependent protein phosphorylation occurs markedly in guard cells, and that Ca²⁺-dependent phosphorylation of 41- and 25-kDa proteins may be catalyzed by MLCK or MLCK-like protein kinase in guard cells.     

C60-fullerenides of ytterbium and lutetium

Cp^#₂Yb (Cp^#=C₅H₄(CH₂)₂NMe₂) has been obtained by reaction of YbI₂(THF)₂ with 2 equiv. of C₅H₄(CH₂CH₂NMe₂)K in THF. The X-ray structure analysis shows a bent structure with intramolecular coordination of both nitrogen atoms to ytterbium. The reaction of C₆₀-fullerene with Cp^#₂Yb leads to the formation of the fullerenide derivative [Cp^#₂Yb]₂C₆₀, which shows an ESR signal in the solid state and in THF solution at room temperature (solid: ΔH = 50 G, G = 1.9992; solution: ΔH = 10 G, G = 2.0001) and a magnetic moment of 3.6 BM. The lutetium fullerenides CpLu(C₆₀)(DME) (3) and Cp^*Lu(C₆₀)(DME)(C₆H₅CH₃) (4), (Cp = η⁵−C₅H₅, Cp^* = η⁵−C₅Me₅), were obtained by reaction of C₆₀ with CpLu(C₁₀H₈) (DME) and Cp^*Lu(C₁₀H₈) (DME) in toluene. Both complexes are paramagnetic (μ_eff = 1.4 and 0.9 BM) and exhibit temperature-dependent ESR signals (293 K: g = 1.992 and 2.0002 respectively).     

Synthesis and histamine H3 receptor activity of 4-(n-alkyl)-1H-imidazoles and 4-(omega-phenylalkyl)-1H-imidazoles

The influence of lipophilic moieties attached to a 4-1H-imidazole ring on the histamine H₃ receptor activity was systematically investigated. Series of 4-(n-alkyl)-1H-imidazoles and 4-(ω-phenylalkyl)-1H-imidazoles were prepared, with an alkyl chain varying from 2–9 methylene groups and from 1–9 methylene groups, respectively. The compounds were tested for their activity on the H₃ receptor under in vitro conditions. For the 4-(n-alkyl)-1H-imidazoles the activity is proportional to chain length, ranging from a pA₂ value of 6.3±0.2 for 4-(n-propyl)-1H-imidazole to a pA₂ value of 7.2±0.1 for 4-(n-decyl)-1H-imidazole. For the series 4-(ω-phenylalkyl)-4H-imidazoles an optimum in H₃ activity was found for the pentylene spacer: 4-(ω-phenylpentyl)-1H-imidazole has a pA₂ value of 7.8±0.1.     

Evidence for the simulaneous translocation of muscarinic acetylcholine receptor and G protein by carbachol

Interactions between guanine nucleotide regulatory proteins (G proteins) and muscarinic acetylcholine receptors (mAChRs) were studied in vivo following carbachol treatment. Rat brain homogenates were separated by high speed ultracentrigation into heavy and light membrane and 300,000 g supernate franctions. The G proteins were partially purified by Sephadex-G200 and heptylamine-Sepharose and the mAChRs by (3,2′-aminobenzhydryloxy)-tropane-(ABT)-affinity chromatographies. Radioligand binding assays showed that acute carbachol induced a biphasic translocation of the mAChRs and G proteins into the light membrane fraction with an initial release at 5–10 min and a second phase at 60 min. Portions of the released mAChRs and the G proteins, were found in the 300,000 g supernates and light membranes and were eluted in the same peak fractions from a Sephadex G-200 column. This dually labelled peak dissociated in the presence of digitonin, suggesting close association between the mAChR and G protein. ABT-affinity chromatography yielded dually labelled mAChR-G protein fractions which eluated as a single radioactive peak on a second ABT column. the partially purified G proteins from these fractions were photoaffinity labelled with 8-azidoguanosine-5′-triphosphate, [γ-³²P]. SDS-PAGE autoradiography revealed the presence of G_0ξ and G_i which may be released simultaneously with the mAChRs from the plasma membrane. In addition, a 110,000 molecular weight polypeptide was dually labelled by [³H]-PrBCM and [γ-³²P]-8-azido-GTP suggesting the presence of a “mAChR-G protein complex.” These findings provide direct evidence for the release of mAChRs and G proteins and a mAChR-G protein complex by agonist occupation of the mAChRs.     

φX174 gene A protein does not cleave at a mouse mitochondrial DNA sequence homologous to the φX and G4 cleavage site

The light strand origin of replication of mouse mitochondrial DNA contains a 30-nucleotide region which is 60% homologous to the 30-nucleotide conserved sequence in φX174 and G4 viral DNAs known to contain the viral gene A protein cleavage site. Gene A protein does not cleave closed circular mouse mitochondrial DNA under conditions in which φX174 closed circular DNA is cleaved.     

A new member of YER057c family in Trypanosoma cruzi is adjacent to an ABC-transporter

Tcp17 is a Trypanosoma cruzi gene located contiguous to the ABC-transporter tcpgp2. The protein contains 160 amino acid residues with a predicted molecular mass of 16.5 kDa. Western blot analysis using a polyclonal antiserum against recombinant TCP17 revealed that the protein is only expressed in the epimastigote form of the parasite; we did not detect the protein either in the amastigote or trypomastigote forms. A sequence comparison of TCP17 showed a remarkable homology with a conserved family of prokaryotic and eukaryotic proteins called YER057c whose function has not yet been characterized. Here, we propose a new signature of this family considering the N-terminal: [IV]–X(4)–[AV]–[AP]–X–[AP]–X(3)–Y–X(9)–[LIVF]–X(2)–[SA]–G–[QS], and the C-terminal: [AT]–R–X(2)–[IVFY]–X–[VC]–X(2)–L–P–X(4)–[LIVM]–E–[IVM]–[DE] motifs. Immunofluorescence and immunoelectron microscopy studies suggest that the protein has a wide distribution in the cell, with a higher concentration in the external side of the plasma membrane, on the Golgi complex and on cytoplasmic vacuoles. Although the physiological function of TCP17 is unknown, its conservation in evolution suggests biological relevance in the parasite.     

Identification of palindromic sequences recognized by restriction endonucleases, as based on the tabularized sequencing data for seven viral and plasmid DNAs

Computer search of DNA sequences for phages φX174, G4, M13 and fd, plasmids pBR322 and pA03, and virus SV40, was employed to prepare tables specifying the size classes and frequencies of DNA segments located between all possible tetra-, penta- and hexanucleotide palindromes. As described earlier (Fuchs et al., 1978), these tables permit identifying sequences recognized by most of the restriction endonucleases. The effect of sequencing errors on the accuracy of the present identification method is evaluated. Only four of the 224 listed sequences do not appear in any of the seven DNAs, leading to discussion (see Appendix) on the natural sequence distribution.