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PubMed1999

Nucleic acid duplex stability: influence of base composition on cation effects.

The effects of counter ion on a nucleic acid duplex stability were investigated. Since a linear free energy relationship for the thermostability of oligonucleotide duplexes between those in 1 M and in 100 mM NaCl-phosphate buffer were observed regardless of whether they are DNA-DNA, RNA-RNA or RNA-DNA duplexes, simple prediction systems for [Delta] G degrees 37as well as T mvalues in 100 mM NaCl-phosphate buffer were established. These predictions were successful with an average error of only 2.4 degrees C for T mand 5. 7% for G degrees 37values. The number of Na+newly bound to a duplex when the duplex forms (-[Delta] n) was significantly influenced by the base composition, and -[Delta] n for d(GCCAGTTAA)/d(TTAACTGGC) was different for MgCl2, CaCl2, BaCl2and MnCl2(from 0.70 to 0.76 with the same order of the duplex stability). Almost no additive effects on the duplex stability was observed for NaCl and MgCl2, suggesting a competitive binding for these cations. The sequence-dependent manner of [Delta] n suggests the presence of preferential base pairs or nearest-neighbor base pairs for the cation binding, which would affect nearest-neighbor parameters.

Base Composition↗
PubMed1990

Sequence-specific chemical modification of chromatin DNA with reactive derivatives of oligonucleotides.

Chemical modification of the chromatin DNA with alkylating derivatives of oligothymidylate (pT)16 and oligoadenylate (pA)16 bearing 4-(N-2-chloroethyl-N-methylamino)benzylphosphamide group at the 5'-phosphate has been investigated. It was found that the derivatives do react with DNA in chromatin. The reactions occur presumably at the complementary sequences of the DNA since the reaction of the oligothymidylate derivative is inhibited by oligonucleotide (pT)16 taken in excess and is not influenced by hexadecanucleotide of a random structure. Isolated DNA does not react with the oligothymidylate derivative. It is concluded that in chromatin, DNA is partially unwound or possesses some sites which can be opened easily in the presence of complementary oligonucleotides.

Alkylating Agents↗
PubMed1993

[Interaction of oligonucleotides with blood serum proteins].

The interaction of alkylating derivatives of deoxyribonucleotides whose 5'-terminal phosphate group contains a 4-[(N-2-chloroethyl-N-methyl)amino]benzylamine residue with serum proteins has been studied. Incubation of whole human sera with various concentrations of the alkylating derivative, p(T)16, resulted in affinity modification of several proteins, among which albumin as well as IgM and IgG were the most readily detectable ones. The type of dependence of the degree of modification of these proteins on oligonucleotide concentration suggests that the oligonucleotides display a higher affinity for IgM than for IgG and albumin. Binding of reactive oligomer derivatives to serum proteins was inhibited by polyanions of different oligomeric composition, two-chain DNA and heparin, the latter being the strongest inhibitor of the immunoglobulins. These data point to a role of nonspecific ion-to-ion interactions in the IgG-oligonucleotide complex formation. Oligonucleotide interaction with murine monoclonal antibodies GI was inhibited by a specific antigen which suggests that oligonucleotides may interact with immunoglobulin either at or near a site where the antigen is recognized by the antibody.

Alkylating Agents↗
PubMed1989

The DNA bending by acetylaminofluorene residues and by apurinic sites.

We have studied the distortions induced in double-stranded oligonucleotides by covalently bound acetylaminofluorene residues and by apurinic sites. Within the acetylaminofluorene-modified oligonucleotide three base-pairs are unpaired as detected by the chemical probes chloroacetaldehyde and osmium tetroxide. These two probes reveal that the bases adjacent to the apurinic site are paired. In both the modified double-stranded oligonucleotides, the backbone on the 5' side of the modification is more reactive with 1,10-phenanthroline copper than the backbone on the 3' side. On polyacrylamide gels, the ligated multimers of acetylaminofluorene or apurinic site-modified oligonucleotides migrate slower than the multimers of the unmodified oligonucleotides. It is suggested that the acetylaminofluorene-modified guanine residues and the apurinic sites behave more as hinge joints than as the centres of directed bends.

2-Acetylaminofluorene↗
PubMed2000

Sequence analysis of domains III and IV of the 23S rRNA gene of verticillate streptomycetes.

Domains III and IV of the 23S rRNA gene of 25 strains of verticillate streptomycetes were sequenced. None of the sequences was identical to any other, with regions of variability being restricted to parts of helices 54 and 64. No relationships were detected between the similarities in the sequence and the assignment to phenetic clusters as defined by the numerical taxonomy studies. Limited agreement was also found between similarity of the sequences and DNA-DNA homology values. However, species (> 70% DNA-DNA homology values)-specific diagnostic oligonucleotides generally could be defined, except for Streptomyces baldaccii. Therefore the determination of the 23S rRNA sequence may be of greater value for fingerprinting individual strains than for taxonomic or identification purposes.

Base Composition↗
PubMed1993

Escherichia coli transcription termination factor rho. I. ATPase activation by oligonucleotide cofactors.

Rho protein is required to bring about RNA release from Escherichia coli transcription complexes paused at specific (rho-dependent) termination sites. Rho functions in termination as a hexamer of identical subunits arranged in D3 symmetry, with each rho subunit carrying an RNA- and an ATP-binding site. The detailed mechanism of rho-catalyzed transcript release remains to be determined, but it is clear that the RNA-dependent ATPase activity that is stimulated by interaction with the nascent transcript is essential to the termination function of rho. In this study, we have used short (8-10 nucleotide residues) synthetic ribo-oligonucleotides to model the interaction of segments of the RNA cofactor with rho. A poly(dC) enhancement procedure was used to permit the measurement of steady state ATPase parameters. We show that (i) ATPase activation is cofactor composition- and sequence-dependent; (ii) at least 60% of the residues of these short RNA cofactors must be cytosine to produce maximal rho ATPase activation; (iii) oligo(rU,rC) cofactors with the rU residues located at the 5' termini of the oligomer are much better ATPase cofactors than oligomers containing rC residues only; (iv) this enhanced stimulation is not observed if the rU residues are replaced by rA residues; (v) this cofactor activity relative to oligo(rC) is reversed if the rU residues are placed at the 3' terminus of RNA oligomer; and (vi) these nucleotide sequence and composition effects do not appear to be functions of K+ or Mg2+ concentration. These ATPase activation results are correlated with the binding to rho of oligonucleotide cofactors in the accompanying paper (Wang, Y., and von Hippel, P. H. (1993) J. Biol. Chem. 268, 13947-13955).

Adenosine Triphosphatases↗
PubMed1985

The DNA restriction endonuclease of Escherichia coli B. II. Further studies of the structure of DNA intermediates and products.

The DNA intermediates and final products formed by the Type I restriction endonuclease, EcoB, were further characterized. DNA cleaved on only one strand (hemi-restricted DNA) contains gaps of approximately 70-100 nucleotides, while the fully restricted products contain 3'-single-stranded tails averaging approximately 70-100 nucleotides for each strand cleaved. The gaps and tails are formed with the release of an equal number of nucleotides as small oligonucleotides that are soluble in acid. After purification, neither the hemi-restricted nor the fully restricted DNAs are cleaved again by EcoB. There is no apparent specificity for which strand of a duplex is initially cleaved by EcoB, nor is there specificity with respect to the composition of the 3'-terminal nucleotide formed on the DNA or the 3'- or 5'-terminal nucleotides of the acid-soluble oligonucleotides released during DNA cleavage. The structure formed at the 5' terminus of the DNA product which blocks phosphorylation by T4 polynucleotide kinase remains unknown, but its removal with phage lambda exonuclease allows at least some reutilization of recognition sites by EcoB as well as phosphorylation of the newly formed 5' termini. To explain the complex mechanism of this enzyme, it is suggested that the unidentified 5'-tails prevent wasteful rerestriction from occurring, whereas the 3'-single-stranded tails create DNA which, when nonhomologous to chromosomal DNA, cannot be rescued because such tails are not substrate for DNA polymerases. However, when homologous chromosomal DNA exists, the randomly cleaved large fragments with these tails can easily be assimilated by recA-mediated genetic recombination, thus stimulating DNA exchange between related organisms.

Animals↗
PubMed1993

A simple method of detecting amplified DNA with immobilized probes on microtiter wells.

We have developed a simple hybridization method for the detection of specific DNA sequences amplified by polymerase chain reaction (PCR). This method is similar to an enzyme-linked immunosorbent assay (ELISA) format in that labeled PCR products at the 5' termini are hybridized with probes immobilized on a microtiter well and the bound PCR products are detected in a manner similar to that of an enzyme immunoassay (EIA). Two improvements have been made in immobilizing the probe to the microtiter wells, in terms of increasing both immobility and hybridization efficiency. One is that single-stranded (ss) DNA, without the complementary strand, is used. The other is that instead of a single copy, a tandem array of the probe is used for immobilization and hybridization. Using of ssDNA containing about a 60-repeat array of a relevant sequence as an immobilized probe, the sensitivity increased 10-fold over that of a single oligonucleotide unit. We also found that the hybridization conditions such as time, temperature, and solution composition could be simplified. Therefore this method is especially suited for handling of a large number of samples, for example detection of viruses, bacteria, and other pathogens, as well as mot human genetic disorders.

Base Sequence↗
PubMed2003

Bacterioplankton community structure in a maritime antarctic oligotrophic lake during a period of holomixis, as determined by denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH).

The bacterioplankton community structure in Moss Lake, a maritime Antarctic oligotrophic lake, was determined with vertical depth in the water column, during the ice-free period on Signy Island in the South Orkney Islands. Bacterioplankton community structure was determined using a combination of direct counting of 4',6-diamidino-2-phenylindole (DAPI) stained cells, PCR amplification of 16S rRNA gene fragments, denaturing gradient gel electrophoresis (DGGE) and in situ hybridization with group-specific, fluorescently labeled oligonucleotide probes. Using PCR amplification of 16S rRNA gene fragments and DGGE, the bacterioplankton community composition was shown to be constant with vertical depth in the water column. Specific bacterioplankton species identified through cloning and sequencing the DGGE products obtained were Flavobacterium xinjiangensis (a Flavobacterium), Leptothrix discophora (a beta-Proteobacterium), and a number of uncultured groups: two beta-Proteobacteria, an unclassified Proteobacterium, three sequences from Actinobacteria, and a Cyanobacterium. Fluorescence in situ hybridization (FISH), however, demonstrated that there were minor but significant fluctuations in different groups of bacteria with vertical depth in the water column. It showed that the beta-Proteobacteria accounted for between 26.4 and 71.5%, the alpha-Proteobacteria 2.3-10.6%, the gamma-Proteobacteria 0-29.6%, and the Cytophaga-Flavobacterium group 1.8-23.5% of cells hybridizing to a universal probe. This study reports the first description of the community structure of an oligotrophic Antarctic freshwater lake as determined by PCR-dependent and PCR-independent molecular techniques. It also suggests that the bacterioplankton community of Moss Lake contains classes of bacteria known to be important in freshwater systems elsewhere in the world.

Antarctic Regions↗
PubMed2003

Dynamics of microbial populations and strong selection for Cycloclasticus pugetii following the Nakhodka oil spill.

Microbial population changes were monitored immediately after the Nakhodka oil spill accident in January 1997 at the heavily oil-contaminated Mikuni coast along the Sea of Japan. The total cell number was almost stable for one year at 2-5 x 10(5) cells mL(-1), while the relative occurrence of culturable heterotrophs and degraders of oil components such as C-heavy oil, kerosene, and n-tetradecane varied, showing a maximum (>50% of the total) immediately following the accident. Gene amplification and phylogenetic analysis of a dilution culture using C-heavy oil as the sole carbon and energy source revealed that one of the predominant oil degraders at the oil-contaminated coast in 2 weeks after the accident closely resembled the aromatic hydrocarbon decomposer Cycloclasticus pugetii. Microbial community composition in oil-contaminated seawater was estimated at the molecular level using newly developed oligonucleotide probes, probe wash-off curve estimation, and quantitative fluorescence dot-blot hybridization techniques. At two different oil-polluted sites, harbor and intertidal regions, the C. pugetii group was estimated to make up 23-25% of the total Bacteria population, followed by the aliphatic hydrocarbon decomposer Alcanivorax borkumensis, which formed 4-7% of the Bacteria. In incubation experiments using floated oil slick and indigenous microbes collected at the harbor, oil degradation activities were enhanced by the addition of both organic and inorganic nutrients. Significant decreases were found in aromatic and aliphatic hydrocarbon fractions: 54-60% and 22-24% in 2 weeks to 68-77% and 23-32% in 2 months, respectively.

Base Sequence↗
PubMed2004

Bacterial community shifts in nonylphenol polyethoxylates-enriched activated sludge.

A molecular approach was used to evaluate the effect of nonylphenol ethoxylate surfactants on the bacterial diversity in lab-scale activated sludge reactors. Separate bench-scale units were fed synthetic wastewater with and without addition of branched nonylphenol ethoxylates (NPnEO). The performance of the reactors, in terms of carbonaceous removal was largely unaffected by the presence of NP10EO in the feeding solution. However, addition of NP10EO exerted a pronounced shift in bacterial community composition. In situ hybridization analyzing larger phylogenetic groups of bacteria with ribosomal RNA-targeted oligonucleotide probes revealed the dominance of clusters composed of Betaproteobacteria, accounting for up to one-third of 4',6-diamidino-2-phenylindol-dihydrochloride (DAPI)-stained cells in NP10EO amended reactors and only 5% of DAPI-stained cells in the controls. These shifts in populations of larger phylogenetic groups were confirmed by dot-blot analysis of rRNA. Members of gamma subclass of Proteobacteria were present in low numbers in all activated sludge samples examined, suggesting that only bacteria affiliated with the beta subclass of Proteobacteria may have a specific role in NP10EO degradation.

Aerobiosis↗
PubMed1992

Structural features of the low-molecular-mass human salivary mucin.

The low-molecular-mass human salivary mucin has at least two isoforms, MG2a and MG2b, that differ primarily in their sialic acid and fucose content. In this study, we characterize further these isoforms, particularly their peptide moieties. Trypsin digests of MG2a and MG2b yielded high- and low-molecular-mass glycopeptides following gel filtration on Sephacryl S-300. The larger glycopeptides from MG2a and MG2b had similar amino acid compositions and identical N-terminal sequences, suggesting common structural features between their peptides. An oligonucleotide probe generated from the amino acid sequence of the smaller glycopeptide from MG2a was employed in Northern-blot analysis. This probe specifically hybridized to two mRNA species from human submandibular and sublingual glands. A cDNA clone selected from a human submandibular gland cDNA expression library with antibody generated against deglycosylated MG2a also hybridized to these two mRNA species. In both cases, the larger mRNA was polydisperse, and the hybridization signal was more intense in the sublingual gland. In addition, the N-terminal amino acid sequence of the larger glycopeptide was found to be part of one of the selected MG2 cDNA clones.

Amino Acid Sequence↗
PubMed1995

The neural cell adhesion molecule (N-CAM) inhibits proliferation in primary cultures of rat astrocytes.

Cell proliferation is a key primary process during neural development and also plays an important role in the regenerative response of neural tissue to injury. It has been reported that glial cell proliferation is, at least in part, controlled by a neuronal signal, possibly involving cell surface molecules. We report here that the addition of purified rat neural cell adhesion molecule (N-CAM) to primary cultures of rat forebrain astrocytes inhibits their proliferation. This inhibitory effect can be elicited in cultures grown in chemically defined serum-free medium or in medium that had been supplemented with growth factors. Polyclonal antibodies to N-CAM or their Fab' fragments elicited a similar inhibitory effect. The magnitude of the inhibitory effect of N-CAM was dependent on cell density: it was maximal at low cell densities and weakened progressively as cells approached confluency. Synthetic peptides with sequences identical to a putative homophilic binding region of N-CAM mimicked the effect of purified N-CAM, while peptides of the same length and amino acid composition but with a randomized sequence did not. The addition of N-CAM antisense oligonucleotides to primary astrocyte cultures for 48 h resulted in reduced levels of N-CAM expression. After N-CAM levels on astrocytes were diminished by this treatment, the antiproliferative effect of N-CAM added to the medium was significantly reduced. The combined results suggest that N-CAM homophilic binding may be involved in the control of glial cell proliferation.

Animals↗
PubMed1993

Hybridization specificity, enzymatic activity and biological (Ha-ras) activity of oligonucleotides containing 2,4-dideoxy-beta-D-erythro-hexopyranosyl nucleosides.

Antisense oligonucleotides with a 2,4-dideoxyhexopyranosyl nucleoside incorporated at the 3'-end and at a mutation site of the Ha-ras oncogene mRNA were synthesized. Melting temperature studies revealed that an A*-G mismatch is more stable than an A*-T mismatch with these hexopyranosyl nucleosides incorporated at the mutation site. The oligonucleotides are stable against enzymatic degradation. RNase H mediated cleavage studies revealed selective cleavage of mutated Ha-ras mRNA. The oligonucleotide containing two pyranose nucleosides at the penultimate position activates RNase H more strongly than natural oligonucleotides. No correlation, however, was found between DNA - DNA or RNA - DNA melting temperatures and RNase H mediated cleavage capacity. Although the A*-G mismatch gives more stable hybridization than the A*-T base pairing, only the oligonucleotides containing an A*-T base pair are recognized by RNase H. This modification is situated 3 base pairs upstream to the cleavage site. Finally, the double pyranose modified oligonucleotide was able to reduce the growth of T24 cells (bladder carcinoma) while the unmodified antisense oligonucleotide was not.

Base Composition↗
PubMed1994

Recognition and cleavage of hairpin structures in nucleic acids by oligodeoxynucleotides.

The possibility of designing antisense oligodeoxynucleotides complementary to non-adjacent single-stranded sequences containing hairpin structures was studied using a DNA model system. The structure and stability of complexes formed by a 17mer oligonucleotide with DNA fragments containing hairpin structures was investigated by spectroscopic measurements (melting curves) and chemical reactions (osmium tetroxide reaction, copper-phenanthroline cleavage). A three-way junction was formed when the oligonucleotide was bound to both sides of the hairpin structure. When the complementary sequences of the two parts of the oligonucleotide were separated by a sequence which could not form a hairpin, the oligonucleotide exhibited a slightly weaker binding than to the hairpin-containing target. An oligodeoxynucleotide-phenanthroline conjugate was designed to form Watson-Crick base pairs with two single-stranded regions flanking a hairpin structure in a DNA fragment. In the presence of Cu2+ ions and a reducing agent, two main cleavage sites were observed at the end of the duplex structure formed by the oligonucleotide-phenanthroline conjugate with its target sequence. Competition experiments showed that both parts of the oligonucleotide must be bound in order to observe sequence-specific cleavage. Cleavage was still observed with target sequences which could not form a hairpin, provided the reaction was carried out at lower temperatures. These results show that sequence-specific recognition and modification (cleavage) can be achieved with antisense oligonucleotides which bind to non-adjacent sequences in a single-stranded nucleic acid.

Base Composition↗
PubMed2006

Impedimetric genosensors for the detection of DNA hybridization.

Impedance spectroscopy is proposed as the transduction principle for detecting the hybridization of DNA complementary strands. In our experiments, different DNA oligonucleotides were used as model gene substances. The gene probe is first immobilized on a graphite-epoxy composite working electrode based genosensor. Detection principle is based on changes of impedance spectra of a redox marker, the ferro/ferricyanide couple, after hybridization with target DNA. Resistance offered to the electrochemical reaction serves as the working signal, allowing for an unlabelled gene assay.

Electric Impedance↗
PubMed1989

The left-handed Z-DNA conformation in oligodeoxynucleotides containing different amounts of AT base pairs: a far UV circular dichroism study.

A number of fully self-complementary oligodeoxynucleotides have been synthesized and examined for their ability to assume the left-handed Z-DNA conformation in high salt solutions. The B- and Z-forms are identified by circular dichroism spectra, covering both the long- (220-300 nm) and short-wavelength (185-220 nm) regions, the latter showing CD bands very useful for identifying the sense of the helix winding. The main results of the study can be summarized as follows: a) sequences composed by AT and CG blocks do support the B to Z transition, even when the AT contents amounts to 50%; b) the occurrence of consecutive purine-purine or pyrimidine-pyrimidine dyads does not inhibit the B to Z transition, although a stronger reduction of water activity is required; c) (AC)n and (GT)n containing oligonucleotides do undergo the B to Z transition in solution; d) a millimolar quantity of Ni2+ concomitant with 5 M NaClO4 is found to be very effective in bringing about the B to Z transition in most of the sequences considered in this study.

Adenine↗
PubMedDate not supplied

[The theory and practice of the creation of antisignature oligodeoxyribonucleotides as universal antimicrobial agents (the principles of a drug technology of the 21st century)].

Gene-directed and anti-sense (mRNA-directed) synthetic oligonucleotides (SO) have a common main shortcoming. That is the necessity to introduce intercalators to their composition for the stronger interaction with targets to prevent their separation from the latter by DNA-polymerase and RNA-polymerase complexes which work on genome or with mRNA by ribosomes moving along them. Intercalation leads to considerable loss of SO selectivity in respect to the target. The author substantiates advantages of another type of SO which action is directed to blocking of the function of signature sequences of ribosomal RNA (rRNA) that completely ceases the self-assembly of ribosomal subunits and totally excludes the process of translation and synthesis of proteins. Such type SO advantages are as follows: a) a short chain which includes 8-13 nucleotides altogether; b) absence of the necessity of intercalation; c) high specificity in respect to targets; d) high stability in respect to nucleases action under modification by one of the methods of internucleotide bonds and, e) a possibility to deliver any microorganism to the cells when allowing for auxotrophy of the latter in respect to one or another substance. It is foreseen that antisignature SO can become most promising among the drugs called to block the functions of nucleic acids of the agents of the disease.

Anti-Bacterial Agents↗