Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA

A series of nucleobase-modified siRNA duplexes containing "rare" nucleosides, 2-thiouridine (s(2)U), pseudouridine (Psi), and dihydrouridine (D), were evaluated for their thermodynamic stability and gene silencing activity. The duplexes with modified units at terminal positions exhibited similar stability as the nonmodified reference. Introduction of the s(2)U or Psi units into the central part of the antisense strand resulted in duplexes with higher melting temperatures (Tm). In contrary, D unit similarly like wobble base pair led to the less stable duplexes (DeltaTm 3.9 and 6.6 degrees C, respectively). Gene-silencing activity of siRNA duplexes directed toward enhanced green fluorescent protein or beta-site APP cleaving enzyme was tested in a dual fluorescence assay. The duplexes with s(2)U and Psi units at their 3'-ends and with a D unit at their 5'-ends (with respect to the guide strands) were the most potent gene expression inhibitors. Duplexes with s(2)U and Psi units at their 5'-ends were by 50% less active than the nonmodified counterpart. Those containing a D unit or wobble base pair in the central domain had the lowest Tm, disturbed the A-type helical structure, and had more than three times lower activity than their nonmodified congener. Activity of siRNA containing the wobble base pair could be rescued by placing the thio-nucleoside at the position 3'-adjacent to the mutation site. Thermally stable siRNA molecules containing several s(2)U units in the antisense strand were biologically as potent as their native counterparts. The present results provide a new chemical tool for modulation of siRNA gene-silencing activity.     

SYNTHESIS AND HYBRIDIZATION OF NOVEL CHIRAL PYRROLIDINE BASED PNA ANALOGUE

Four different PNA fragments containing units of either the R- or S- isomer of N-(2-pyrrolidine-methyl)-N-(thymine-1-acetyl)-glycine (Pmg) were synthesized on a solid support. UV thermal melting experiments with complementary RNAs were performed and it was found that R-Pmg containing PNAs bind better to RNA than those containing the S-Pmg units.     

The abundance of additional N-acetyllactosamine units in N-linked tetraantennary oligosaccharides of human Tamm-Horsfall glycoprotein is a donor-specific feature

Previously, treatment of Tamm-Horsfall glycoprotein (THp) from different donors with endo-beta-galactosidase has been shown to liberate a tetra- and a Sd(a)-active pentasaccharide, concluding the presence of N-linked carbohydrate chains containing additional N - acetyllactosamine units. These type of oligosaccharides were not found in a detailed structure elucidation of the carbohydrate moiety of THp of one male donor, suggesting a donor-specific feature for these type of structures. Therefore, THp was isolated from four healthy male donors and each subjected to endo-beta-galactosidase treatment in order to release these tetra- and Sd(a)-active pentasaccharide. Differences were observed in the total amount of released tetra- and Sda-active pentasaccharide of the used donors (42, 470, 478, 718 microg/100 mg THp), indicating that the presence of repeating N-acetyllactosamine units incorporated into the N-glycan moiety of THp is donor specific. Furthermore, a higher expression of the Sd(a) determinant on antennae which display N-acetyllactosamine elongation was observed, suggesting a better accessibility for the beta-N-acetylgalactosaminyltransferase. In order to characterize the N-glycans containing repeating N- acetyllactosamine units, carbohydrate chains were enzymatically released from THp and isolated. The tetraantennary fraction, which accounts for more than 33% of the total carbohydrate moiety of THp, was used to isolate oligosaccharides containing additional N - acetyllactosamine units. Five N-linked tetraantennary oligosaccharides containing a repeating N-acetyllactosamine unit were identified, varying from structures bearing four Sd(a) determinants to structures containing no Sd(a) determinant (see below). One compound was used in order to specify the branch location of the additional N- acetyllactosamine unit, and it appeared that only the Gal-6' and Gal-8' residues were occupied by a repeating N -acetyllactosamine unit.      

Olefinic peptide nucleic acid (OPA)

The olefinic peptide nucleic acid analogues (OPA) monomers containing the bases thymine and adenine were synthesised in 11 steps. Fully modified oligomers containing these units were prepared and their pairing properties assessed by means of UV-melting experiments.     

Nucleotide sequence of a glucosyltransferase gene from Streptococcus sobrinus MFe28.

The complete nucleotide sequence was determined for the Streptococcus sobrinus MFe28 gtfI gene, which encodes a glucosyltransferase that produces an insoluble glucan product. A single open reading frame encodes a mature glucosyltransferase protein of 1,559 amino acids (Mr, 172,983) and a signal peptide of 38 amino acids. In the C-terminal one-third of the protein there are six repeating units containing 35 amino acids of partial homology and two repeating units containing 48 amino acids of complete homology. The functional role of these repeating units remains to be determined, although truncated forms of glucosyltransferase containing only the first two repeating units of partial homology maintained glucosyltransferase activity and the ability to bind glucan. Regions of homology with alpha-amylase and glycogen phosphorylase were identified in the glucosyltransferase protein and may represent regions involved in functionally similar domains.     

Large inverted duplications are associated with gene amplification

Amplified DNA can be found in arrays of large repeated units, with each repeat unit containing a marker gene and surrounding DNA sequences. Amplified DNA sequences from established cell lines were assessed for the presence of repeat units in the form of inverted duplications. Inverted duplicated DNA was detected by virtue of its concentration-independent resistance to S1 hydrolysis after denaturation and rapid renaturation. Using this assay, inverted duplications were detected in amplified DNA (both DM and HSR configurations) containing the myc gene (16-50 copies/cell) in four human tumor cell lines and in amplified DNA containing the CAD gene (30-200 copies/cell) in three PALA-resistant BHK cell lines. The widespread association of inverted duplications with amplified DNA must bear on the amplification mechanism.     

Galactomannans with novel structures from the lichen Roccella decipiens Darb

Two homogeneous galactomannan fractions were isolated from the lichen, Roccella decipiens, one (FP) containing Man and Gal in an 81:19 molar ratio and the other (RFS), having Man, Gal, and Glc in a 43:56:1 molar ratio. FP consisted of a main chain with (1-->4)-linked alpha-D-Manp units, most of which were substituted at O-2 with side chains consisting of nonreducing end-, 2-O- and 6-O-substituted alpha-Manp units. The latter appeared to be substituted by single-unit beta-D-Galf nonreducing ends. RFS contained a similar alpha-D-Manp core structure, but with side chains containing nonreducing end, 5-O-, 6-O-, and 5,6-di-O-substituted beta-D-Galf units. Such polysaccharide structures have not been previously reported.     

Preparation of chondroitin sulfate libraries containing disulfated disaccharide units and inhibition of thrombin by these chondroitin sulfates

Chondroitin sulfate (CS) containing GlcA-GalNAc(4,6-SO₄) (E unit) and CS containing GlcA(2SO₄)-GalNAc(6SO₄) (D unit) have been implicated in various physiological functions. However, it has been poorly understood how the structure and contents of disulfated disaccharide units in CS contribute to these functions. We prepared CS libraries containing E unit or D unit in various proportions by in vitro enzymatic reactions using recombinant GalNAc 4-sulfate 6-O-sulfotransferase and uronosyl 2-O-sulfotransferase, and examined their inhibitory activity toward thrombin. The in vitro sulfated CSs containing disulfated disaccharide units showed concentration-dependent direct inhibition of thrombin when the proportion of E unit or D unit in the CSs was above 15–17%. The CSs containing both E unit and D unit exhibited higher inhibitory activity toward thrombin than the CSs containing either E unit or D unit alone, if the proportion of the total disulfated disaccharide units of these CSs was comparable. The thrombin-catalyzed degradation of fibrinogen, a physiological substrate for thrombin, was also inhibited by the CS containing both E unit and D unit. These observations indicate that the enzymatically prepared CS libraries containing various amounts of disulfated disaccharide units appear to be useful for elucidating the physiological function of disulfated disaccharide units in CS.     

First isolation and structural determination of cyclic beta-(1-->2)-glucans from an alga, Chlorella pyrenoidosa

The aqueous extract of the edible green microalgae Chlorella pyrenoidosa is of interest because of its immunostimulatory activity. Some components in the extract have been identified previously, namely a unique type of arabinogalactan and a galactofuran. Further fractionation of this extract was accomplished by treating the aqueous solution of the fraction precipitated by addition of 1.5vol of 95% ethanol with cetyltrimethylammonium bromide. The residue obtained by concentration of the supernatant was fractionated further by anion-exchange chromatography and size-exclusion chromatography on Sephadex G-100. Two fractions from the latter column were retained, of which one was a starch-like alpha-(1-->4)-linked d-glucan with some alpha-(1-->6) branches, and the other contained a starch plus a mixture of beta-(1-->2)-d-glucans. ESI mass spectrometry was used to show that the mixture contained both cyclic and linear beta-(1-->2)-d-glucans in a cyclic:linear ratio of 64:36, based on intensities of mass spectral peaks. For the cyclic beta-(1-->2)-d-glucans, ring sizes ranged from 18 to 35 monosaccharides with the ring containing 21 glucose units (54% of the cyclic glucans) being greater than three times more abundant than the next most abundant component, the ring containing 22 glucose units (15%). No rings containing 20 glucose units were present. This is the first observation of cyclic beta-(1-->2)-d-glucans in algae, as far as we are aware. For the linear beta-(1-->2)-d-glucans, the component containing 20 glucoses was most abundant (35% of the linear glucans), while the component containing 21 glucose units was the next most abundant (17%). These relatively low-molecular-weight glucans had low immunostimulatory activity.     

Novel amphiphilic poly(epsilon-caprolactone)-g-poly(L-lysine) degradable copolymers

As part of the search of novel degradable polymers, amphiphilic and cationic poly(epsilon-caprolactone)-g-poly(l-lysine) (PCL-g-PlL) copolymers have been synthesized following a grafting "onto" or a grafting "from" method both applied to a macropolycarbanionic PCL derivative. The first approach led to PCL-g-PZlL containing 36% of epsilon-caprolactone and 64% of N-epsilon-Z-l-lysine units, by reaction of activated poly(N-epsilon-Z-l-lysine) on the macropolycarbanion derived from PCL. The second route was based on the anionic ring opening polymerization of N-carboxyanhydride of N-epsilon-benzyloxycarbonyl-l-lysine initiated by the macropolycarbanion derived from PCL and led to a similar copolymer containing 45% of of epsilon-caprolactone and 55% of N-epsilon-Z-l-lysine units. After deprotection of the lysine units, PCL-g-PlL copolymers were obtained. These copolymers are water-soluble and form nanometric micelle-like objects with mean diameters between 60 and 500 nm in distilled water depending on the synthesis route.     

Accumulation of a poly(hydroxyalkanoate) copolymer containing primarily 3-hydroxyvalerate from simple carbohydrate substrates by Rhodococcus sp. NCIMB 40126

A number of taxonomically-related bacteria have been identified which accumulate poly(hydroxyalkanoate) (PHA) copolymers containing primarily 3-hydroxyvalerate (3HV) monomer units from a range of unrelated single carbon sources. One of these, Rhodococcus sp. NCIMB 40126, was further investigated and shown to produce a copolymer containing 75 mol% 3HV and 25 mol% 3-hydroxybutyrate (3HB) from glucose as sole carbon source. Polyesters containing both 3HV and 3HB monomer units, together with 4-hydroxybutyrate (4HB), 5-hydroxyvalerate (5HV) or 3-hydroxyhexanoate (3HHx), were also produced by this organism from certain accumulation substrates. With valeric acid as substrate, almost pure (99 mol% 3HV) poly(3-hydroxyvalerate) was produced. N.m.r. analysis confirmed the composition of these polyesters. The thermal properties and molecular weight of the copolymer produced from glucose were comparable to those of PHB produced by Alcaligenes eutrophus.     

Monoterpene glycosides isolated from Fadogia agrestis

Six monoterpene glycosides were isolated from Fadogia agrestis. Their structures were elucidated using a combination of mass spectroscopy, 1D- and 2D-homo- and hetero-NMR spectroscopy and chemical analysis, and established as being derivatives of 2,6-dimethyl-2(E),6(Z)-octadiene-1,8-diol containing from two to four units of rhamnopyranose and, three of them, one or two additional units of glucopyranose. In three of the compounds an acyl group of 8-hydroxy-2,6-dimethyl-2(E),6(Z)-octadienoyl was found esterifying the O-2 position of one of the units of rhamnopyranose.     

Olefinic Peptide Nucleic Acid (OPA)

Abstract

The olefinic peptide nucleic acid analogues (OPA) monomers containing the bases thymine and adenine were synthesised in 11 steps. Fully modified oligomers containing these units were prepared and their pairing properties assessed by means of UV-melting experiments.     

13C-n.m.r. studies of monomeric composition and sequence in alginate

High-resolution, ¹³C-n.m.r. spectra of slightly depolymerised alginates have been interpreted. The sequence of monomer units, l-guluronate (G) and d-mannuronate (M), markedly influenced the chemical shifts. At 50 MHz, some of the individual carbon resonances of both units were resolved into four lines, in evident dependence upon the identities of the units immediately preceding and following them in the chains. The relative intensifies of the signals permitted rapid computation of (1) monomeric composition (M/G ratio), (2) monomeric sequence in terms of a complete set of four diad and eight triad frequencies, and (3) the composition (M/G ratio) of end units and of the units adjacent to M-residues at the non-reducing end. The diad frequencies indicated that alginate was a block co-polymer containing number-average, co-monomer block-lengths of ～2?8. The triad frequencies indicated average lengths of ～4?8 for blocks containing two or more units, these being somewhat longer for G- than for M-blocks. Regions of the chains having a strictly alternating sequence of M- and G-residues were short. The relative occurrence of G-centred triads deviated significantly from those predicted by first-order Markovian statistics.     

Identification and quantification of dolichol and dolichoic acid in neuromelanin from substantia nigra of the human brain

Neuromelanin (NM) isolated from the substantia nigra of the human brain is found to contain a series of dolichoic acids (dol-CA) containing 14-20 isoprene units. This is the first observation of dol-CA in a natural system. Using internally spiked nor-dolichol and nor-dolichoic acid standards, the concentrations of dolichol (dol) and dol-CA present in NM were determined. Remarkably, dol was only four times as abundant as dol-CA in NM. The distribution of dol-CA chains lengths in NM also differed from that of dol, suggesting that the enzyme(s) responsible for the conversion of dol to dol-CA prefer a dolichol substrate containing 19 isoprene units.     

A survey of the accumulation of novel polyhydroxyalkanoates by bacteria

Summary A wide range of bacterial strains were examined for their ability to accumulate polyhydroxyalkanoates (PHA) from various carbon sources. Strains were selected from those reported to accumulate poly-3-hydroxybutyrate (PHB), related organisms and laboratory stocks. Other strains known to utilize n-alkanes, n-alcohols or n-acids were chosen to investigate their ability to produce long-chain PHAs. Five strains accumulated only PHB, 13 accumulated PHAs containing only C₄ and C₅ units and 7 accumulated PHAs containing 3-hydroxyacid units in the range C₅ to C₁₀.     

Bacteriological examination of a modern animal house containing small laboratory animals.

Floors and other areas totalling 1800 m2, comprising conventional and specified-pathogen-free (SPF) units, were screened bacteriologically 6 times in a year. The contamination indices observed were lower within than outside the units, and lower in the SPF than in the conventional unit. Bacterial counts in rooms containing animals in the conventional and SPF units were very similar. In all of the areas investigated within the units, most of the samples revealed less than 2 colony forming units per cm2. In contrast, high degrees of bacteriological contamination were detected in the changing rooms after showering or washing before entry. Staphylococcus epidermidis was the dominant bacterial species isolated. The bacteriological spectrum did not vary between the areas surveyed.     

5—羟色胺对大鼠下丘脑脑薄片室旁核神经元自发电活动的作用

在20个下丘脑脑片上,用玻璃微电极细胞外记录了46个室旁核神经元的自发放电单位,观察了5-羟色胺对它们的作用。当薄片用含5-羟色胺(10~(-6)mol/L)的人工脑脊液灌流后,有16个单位放电频率明显增加,反应的潜伏期为1.21±1.21 min。这种反应可被5-羟色胺的阻断剂噻庚啶所阻断。3个单位放电频率明显减少,27个单位无明显反应。实验结果表明约1/3的下丘脑室旁核神经元能被5-羟色胺所激活。     

New structural features of the polysaccharide from gum ghatti (Anogeissus latifola)

Methylation and 13C NMR analyses were carried out on the high-arabinose, acidic heteropolysaccharide of gum ghatti and the products obtained on three successive, controlled Smith degradations. The side chains contained mainly 2-O- and 3-O-substituted Araf units. Of these the second degradation eliminated remaining alpha-Araf units, and their beta anomers became evident. The proportion of Galp units gradually increased in the form of nonreducing end- and Galp units, although 3,6-di-O- and 3,4,6-tri-O-substituted Galp units diminished. After three degradations groups with consecutive 3-O-substituted beta-Galp units were formed. The proportion of periodate-resistant 3-O- and 2,3-di-O-substituted Manp units was maintained. As a guide to side-chain structures in the polysaccharide, seven of the 10 free reducing oligosaccharide fractions (PC) present in the gum were isolated and examined (NMR, ESIMS, and sometimes methylation analysis). Characterized are alpha-Araf-(1 --> 2)-Ara and three Ara-containing oligosaccharide fractions containing 2-O- and 3-O-substituted units. These gave respectively, ESIMS molecular ions arising from Ara(2), beta-Araf oligosaccharides with four units, beta-Araf oligosaccharides with seven units, and Hex(2)-Ara(4). Alpha-Rhap-(1 --> 4)-GlcA, alpha-Rhap-(1 --> 4)-beta-GlcpA-(1 --> 6)-Gal, and alpha-Rhap-(1 --> 4)-beta-GlcpA-(1 --> 6)-beta-Galp-(1 --> 6)-Gal represented other side chains.     

Ribosomal DNA clusters in pulsed-field gel electrophoretic analysis of human acrocentric chromosomes

For determination of the extent to which ribosomal DNA (rDNA0 is organized in tandemly repeated arrays, cellular DNA was digested with a restriction enzyme (EcoRV) that does not cut within the single 44-kb rDNA unit, and fragments separated by PFGE were hybridized to specific rDNA probes. A series of bands large enough to contain 15 to more than 30 rDNA repeat units was observed. In YACs containing cloned rDNA, however, such clusters were not observed, presumably because, as shown here for a clone starting with 1.5 tandem repeat units, there is a tendency for repeat units to delete out of the insert. By comparative gel electrophoretic analyses of DNAs from rodent hybrid cells containing singly isolated human chromosomes, most of the bands seen in total human DNA were assigned to at least one of the acrocentric chromosomes. Thus, large characteristic assemblies of DNA containing rDNA and lacking EcoRV sites were stable enough to be conserved in some human/rodent hybrid lines. When further digested with HindIII, which cuts rDNA at several points, the rDNA in each band yielded the expected fragments. If the large species consist completely of clusters of tandemly repeated rDNA units, they account for about half of the total cellular rDNA content estimated by saturation hybridization measurements.