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PubMed1983

Targeted random mutagenesis: the use of ambiguously synthesized oligonucleotides to mutagenize sequences immediately 5' of an ATG initiation codon.

The nine base pairs immediately 5' of the initiation codon for the bovine growth hormone (BGH) structural gene have been mutagenized. The mutagenesis method employs the ligation of an ambiguously synthesized oligonucleotide duplex into a previously engineered gap in an expression plasmid for BGH. The mutation method, coupled with hybridization screening, is efficient at isolating 1 and 2 base pair changes within the targeted region. The E. coli cultures harboring the mutant plasmids were assayed for relative levels of BGH expression. The most notable result is the varied effect of substitution of G into the mRNA at various positions in this region.

Animals↗
PubMed1999

Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine Arctic sediments.

Thirteen psychrophilic sulfate-reducing isolates from two permanently cold fjords of the Arctic island Spitsbergen (Hornsund and Storfjord) were phylogenetically analyzed. They all belonged to the delta subclass of Proteobacteria and were widely distributed within this group, indicating that psychrophily is a polyphyletic property. A new 16S rRNA-directed oligonucleotide probe was designed against the largest coherent cluster of these isolates. The new probe, as well as a set of available probes, was applied in rRNA slot blot hybridization to investigate the composition of the sulfate-reducing bacterial community in the sediments. rRNA related to the new cluster of incompletely oxidizing, psychrophilic isolates made up 1.4 to 20.9% of eubacterial rRNA at Storfjord and 0.6 to 3. 5% of eubacterial rRNA at Hornsund. This group was the second-most-abundant group of sulfate reducers at these sites. Denaturing gradient gel electrophoresis and hybridization analysis showed bands identical to those produced by our isolates. The data indicate that the psychrophilic isolates are quantitatively important in Svalbard sediments.

Arctic Regions↗
PubMed1993

A model for the solution structure of a branched, three-strand DNA complex.

The solution structure of a DNA three-way junction (TWJ) containing two unpaired thymidines was elucidated using two- and three-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. TWJs with unpaired nucleotides are ubiquitous structural motifs of complex single-stranded nucleic acids. In the presence of Mg2+, the TWJ complex adopts a unique conformation in which the bases of one of the oligonucleotides ("strand 1") are continuously stacked across the junction. Guanosine 8 of strand 3 (S3-G8), which pairs with S1-C5, stacks on S2-G5, which is paired to S1-C6. The unpaired thymidine bases (S3-T6 and S3-T7) are exposed to the solvent, whereas the sugar of S3-G8 is largely buried. S3-T6 also interacts with the sugar residue of S3-G11. All three stems conform to B-type DNA.

Base Composition↗
PubMed1993

Geometries and energies of Watson-Crick base pairs in oligonucleotide crystal structures.

We analyzed geometries and energies of 469 GC and 224 AT pairs occurring in 11 A-, 54 B- and 12 Z-DNA crystal structures. The most frequent hydrogen bond length conforms to the canonical value but distributions of the hydrogen bond lengths are unexpectedly wide. The average GC pair is rather compressed and opened into the double helix minor groove while an average AT pair has canonical dimensions. The extreme base pair geometrical parameters are the following: buckle -26 degrees and 39 degrees, propeller -33 degrees and 26 degrees, opening -23 degrees and 19 degrees, shear -1.4 A and 2.1 A, stretch -0.7 A and 0.4 A, and stagger -2.3 A and 1.8 A. The analyzed set contains complementary bases apparently bound by unusual bifurcated hydrogen bonds. The unusual base pairing geometries are of two kinds. In the first case, an extreme value of one parameter is compensated for by other geometrical parameters so that the energy of the resulting geometry is acceptable. However, there are also examples when the compensatory effect is missing and then the base pairing instability is dramatic. The most extensive base pair deformations occur in dodecamers, the d(GGATGGGAG) nonamer, the r(UUAUAUAUAUAUAA) 14-mer, and the d(ICCGG) tetramer whose common feature is a low structure resolution. However, very unstable base pairs are also present in the decamer d(CCAACGTTGG) and hexamer d(CGTACG) whose structures were solved at a relatively high resolution. As the deformations probably originate from crystal packing forces and/or data and refinement errors, we recommend to omit these structures from studies of DNA sequence-structure relationships. The remaining hexamers, octamers and decamers whose list and their Watson-Crick base pair characteristics are given in the article are suitable for this purpose because they exhibit no prohibitive energy deviations from the canonical hydrogen bonding properties.

Base Composition↗
PubMed1992

Regional distribution of cells expressing glycine receptor alpha 2 subunit mRNA in the rat brain.

The alpha 2 subunit of the glycine receptor is expressed transiently in the rat brain during early development suggesting that this subunit may be replaced by the alpha 1 subunit in the adult brain. The expression of glycine receptor alpha 2 subunit mRNA was investigated in the 7-day-old rat brain by in situ hybridization histochemistry using oligonucleotide probes specific for this subunit. Neurons expressing alpha 2 subunit mRNA were found to be widely and abundantly distributed throughout brain. We compared the distribution of neurons expressing alpha 2 subunit mRNA with that of neurons expressing alpha 1 or beta subunit mRNA. In the lower brainstem, the location of the neurons expressing alpha 2 subunit mRNA was very similar to that of the neurons with alpha 1 or beta subunit mRNA. Neurons expressing beta subunit mRNA were widespread and numerous in the forebrain, where neurons with alpha 1 subunit mRNA were uncommon. The locations of the neurons labeled by the alpha 2 probe were very similar to those of the cells labeled by the beta probe. These findings suggest that the alpha 2 subunit is not only expressed by immature neurons containing the alpha 1 subunit, but is also common to most immature neurons having the glycine receptor. However, it should be noted that several neurons contained beta and/or alpha 1 subunit mRNA but lacked alpha 2 subunit mRNA, suggesting that the glycine receptor is heterogeneous in its composition during brain development.

Animals↗
PubMed1994

Selection of oligonucleotide probes and experimental conditions for multiplex hybridization experiments.

Different DNA probes hybridize under different conditions. I examine the constraints of the design of oligonucleotide probes that are meant to hybridize to different unique sites in human genomic DNA under a single set of hybridization conditions as a parallel array. In 522 kb of human genomic DNA, 75% of 12-base and 89% of 22-base are unique, as opposed to 90% and 100% as expected of unstructured DNA, and this is not due solely to repetitive elements in the DNA. Hybridization in TMAC to reduce A+T content effects on melting temperature allows only 90% of unique targets to be hybridized under one set of conditions if a 2 degrees C difference between matched and mismatched sequences is required. Standard hybridization conditions allow no more than 60% of unique probes to be used together. This suggests that probe, hybridization conditions, and instrument design for multiple-probe hybridization applications will be harder than previously suggested.

Base Composition↗
PubMed2005

NMR studies on self-complementary oligonucleotides conjugated with methylene blue.

A carboxyl-functionalized methylene blue (MB) derivative was synthesized and covalently coupled to three CG-rich self-complementary 2'-deoxyoligonucleotides at their 5'-end. Thermodynamic and structural details about the interactions between the dye and oligonucleotide duplexes were investigated employing ultraviolet (UV) melting and (1)H nuclear magnetic resonance (NMR) experiments. In contrast to previous findings on MB binding, no specific intercalation or binding in the minor or major groove of the double helix was found in a 100 mM NaCl buffer. Rather, proton chemical shift changes in the conjugates provide ample evidence for weak dye-DNA interactions largely through external MB stacking on the terminal base pairs.

Base Composition↗
PubMed1994

A kinetic and thermodynamic framework for the hammerhead ribozyme reaction.

A hammerhead ribozyme (HH16) with eight potential base pairs in each of the substrate recognition helices stabilized product binding sufficiently to enable investigation of the ligation of oligonucleotides bound to the ribozyme. All individual rate constants for product association and dissociation were determined. The following conclusions were obtained for HH16 from the analysis performed at 50 mM Tris, pH 7.5, 10 mM MgCl2, and 25 degrees C. (1) HH16 cleaves bound substrate with a rate constant of k2 = 1 min-1, similar to rate constants obtained with other hammerhead ribozymes. (2) k-2, the rate of ligation of the 5' product and 3' product to form substrate, equaled 0.008 min-1, indicating an approximately 100-fold preference for the formation of products on the ribozyme. This internal equilibrium, compared with that for the overall solution reaction, gives an effective concentration (EC) of 10(-2) M for the two products bound to the ribozyme. This low EC suggests that upon cleavage of S the hammerhead complex acquires a "floppiness" which provides an entropic advantage for the formation of products on the ribozyme. (3) Product and substrate association rate constants were in the range of 10(7)-10(8) M-1 min-1, comparable to values determined for short helices. (4) The stabilities of ribozyme/product complexes were similar to affinities predicted from helix-coil transitions of simple RNA duplexes, providing no indication of additional tertiary interactions. The products, P1 and P2, stabilize one another 4-fold on the ribozyme. (5) The dissociation constant for the binding of the substrate to the ribozyme was estimated to be about 10(-17) M. These results allowed the construction of a free energy profile for the reaction of HH16, and provide a basis for future mechanistic studies.

Base Composition↗
PubMedDate not supplied

The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence-specific DNA structure variations.

Curved DNA fragments have a reduced electrophoretic mobility in polyacrylamide gels. The retardation in gels is extremely sensitive to small structural variations which influence the DNA helix axis. This gel assay can also be used to detect very small structural variations in DNA sequences which are not curved: The noncurved sequences of interest can be combined with curved stretches in phase with the helix turn. Using such sequence constructions, even subtle influences on the DNA helix axis can be detected. Experiments of this kind allow the determination of a relative order of sequence-specific DNA twist and wedge angles.

Base Composition↗
PubMed2002

Sp1 and Sp3 activate the testis-specific histone H1t promoter through the H1t/GC-box.

The testis-specific linker histone H1t gene is transcribed exclusively in mid to late pachytene primary spermatocytes. Tissue specific expression of the gene is mediated in large part through elements located within the proximal promoter. Previous work in transgenic animals showed that a unique 40 bp promoter element designated H1t/TE is essential for spermatocyte-specific expression. The H1t/TE element contains a GC-box, which is a perfect consensus binding site for members of the Sp family of transcription factors. We have shown that Sp1 and Sp3 are present in testis cells from 9-day-old and adult rats and in pachytene primary spermatocytes and early spermatids and that they can bind to the H1t/GC-box. Mutagenesis of the GC-box reduced H1t promoter activity. Furthermore, a CpG dinucleotide within the GC-box was totally unmethylated in rat testis primary spermatocytes where the gene is transcribed but it was methylated in liver where the gene is silenced. These previous studies supported the importance of the GC-box and suggested that Sp transcription factors contribute to expression of the H1t gene. In this study, we show that co-transfection of Sp1 and Sp3 expression vectors leads to an upregulation of histone H1t promoter activity in several cell lines including testis GC-2spd cells. However, very low H1t promoter activity is seen in GC-2spd cells grown at 39 degrees C, which correlates with lower levels of Sp1 and Sp3 in these cells grown at this elevated temperature. Upregulation of the H1t promoter by Sp1 and Sp3 was also seen in cotransfected NIH3T3 and C127I cell lines. On the other hand, co-transfection of the Sp1 and Sp3 expression vectors does not lead to upregulation of activity of the cell-cycle dependent histone H1d promoter.

Animals↗
PubMed1996

Hairpin antisense oligonucleotides containing 2'-methoxynucleosides with base-pairing in the stem region at the 3'-end: penetration, localization, and Anti-HIV activity.

Hairpin antisense oligodeoxyribonucleotides containing 2'-methoxynucleosides were more active in the micromolar concentration range than linear and DNA hairpin phosphorothioate oligonucleotides with the same sequence. Furthermore, the abilities of hairpin antisense and random hairpin phosphorothioate oligonucleotides to inhibit HIV-1 replication were examined. Antisense oligonucleotides inhibit the replication and the expression of HIV-1 more efficiently than random-oligomers of the same length or with the same internucleotide modification. Four different target sites (gag, pol, rev, and tat) within the HIV-1 genome were studied with regard to the inhibition of HIV-1 replication by antisense oligonucleotides. Antisense oligomers complementary to the sites of the initiation sequences of gag were most effective. The [32P]-labeled hairpin phosphorothioate oligonucleotide was rapidly assimilated by MOLT-4 cells, whereas the [32P]-labeled hairpin phosphodiester oligonucleotide was not. In MOLT-4 cells treated with the FITC-hairpin phosphorothioate oligonucleotide containing 2'-methoxynucleosides by a confocal laser scanning microscope, diffuse fluorescence was observed in the cytoplasm. Interestingly, fluorescent signals accumulated in the nuclear region of chronically infected MOLT-4/HIV-1 cells after a 60 min incubation.

Antiviral Agents↗
PubMed2006

Diferential gene expression and adiposity reduction induced by ascorbic acid supplementation in a cafeteria model of obesity.

Obesity is considered as an inflammatory disease, in which free radical-induced oxidative stress and excessive intake of macronutrients exacerbate their symptoms. In this context, we assessed in rats the possible preventive effect of the supplementation with an antioxidant molecule, ascorbic acid, in order to reduce the adiposity induced by the intake of a high-fat diet. For this purpose, during 56 days, three groups of male Wistar rats were fed on: a) standard pelleted diet, b) Cafeteria diet, c) ascorbate-supplemented (750 mg/kg of body weight) Cafeteria diet. At the end of the experimental period, microarray analysis was used to identify genes transcriptionally induced or repressed by both experimental dietary models (Cafeteria diet supplemented or not with ascorbic acid) in subcutaneous adipose tissue. Dietary ascorbic acid was able to protect against high fat diet effects, reducing the increase of body weight, total body fat and enlargement of different adipose depots induced by the Cafeteria diet without affecting food intake. An association analysis accurately and differentially allowed the detection of gene expression changes related with adiposity and insulin resistance. The genes that more strongly correlated with body fat and HOMA insulin resistance index were involved in adipocyte differentiation, lipid and glucocorticoid metabolism, cell cycle regulation, as well as in several insulin-induced processes. Some other transcripts are regulated by the vitamin C-mediated reduction of adiposity, such as genes that participate in glucocorticoid metabolism, adipogenesis, pentose phosphate pathway, or tricarboxylic acid cycle. This strategy was able to link variations in adipose tissue gene expression with markers of diet-induced obesity in rats, such as insulin resistance and body fat content.

Animals↗
PubMed2004

Quantifying bacterial population dynamics in compost using 16S rRNA gene probes.

Composting provides a dynamic setting for studying ecological topics such as succession, competition, and community stability in a relatively short period of time. This study used hierarchical small sub-unit-based rRNA gene probes to quantify the change in the relative abundance of phylogenetic groups common to compost in laboratory scale reactors. Bacterial 16S rRNA gene targets accounted for only 37% of all small subunit (SSU) rRNA genes initially, but increased to a maximum of 83% of the total at 84 h. The sum of rRNA genes detected using probes specific to Pseudomonas and low-G+C Gram-positive rRNA genes represented between 16% and 87% of the total. The lack of hybridization to the taxon-specific probes was most pronounced between 36 h and 60 h, when the pH was between 4.6 and 4.8. During this period the relative abundance of taxon-specific gene targets accounted for only 17-33% of the total bacterial rRNA gene targets. Pseudomonas-type 16S rRNA genes were the most abundant of the groups measured until 72 h. Those genes had their highest relative abundance at 12 h (78% of bacterial rRNA genes; 30% of all rRNA genes), after which time their relative abundance began to decline as the temperature increased. Prior to 72 h, 16S rRNA genes from low-G+C Gram-positive bacteria (LGC-GPB) represented less than 7% of the bacterial rRNA genes. However, by 84 h the relative abundance of LGC-GPB and Bacillus rRNA genes had increased to 60% and 18% of the bacterial rRNA gene targets, respectively (50% and 15% of all rRNA genes, respectively).

Base Composition↗
PubMed1990

Yeast precursor ribosomal RNA. Molecular cloning and probing the higher-order structure of the internal transcribed spacer I by kethoxal and dimethylsulfate modification.

Plasmids were constructed in which a HindIII fragment of rDNA (6.4 x 10(3) base-pairs) was inserted into vectors pGEM-1 and 2 in both orientations. The DNA insert encoded the yeast 35 S precursor rRNA beginning 180 bases upstream from the 5' end of the mature 18 S rRNA and ending 289 bases beyond the 3' end of the mature 25 S rRNA. The precursor rRNA molecules produced in vitro consisted of 6430 nucleotides, with about 15 residues derived from the Gemini vector on both ends. The general extent of secondary structure of the precursor rRNA was examined by ethidium fluorescence and compared to that of the mature rRNAs. Both precursor and mature rRNAs responded similarly to changes in magnesium ion concentration and to digestion by cobra venom and T1 ribonucleases. The higher-order structure of the internal transcribed spacer-1 (ITS-1) region of the 35 S rRNA molecule was further examined by kethoxal and dimethylsulfate modifications and primer extension. Accessible adenine and guanine residues were located by primer extension analysis with avian myeloblastosis virus reverse transcriptase. On the basis of experimental data and computer-generated structures, a secondary structure model was proposed for the ITS-1 region. In this model, six hairpin stems involving adjacent nucleotides are present. A long-range interaction between nucleotides at the middle of the ITS-1 region and an, as yet, unidentified sequence located at another region of the precursor rRNA is suggested also. A candidate for this interacting sequence is that previously proposed, on a theoretical basis, to be involved in the removal of the precursor 18 S rRNA species for 35 S precursor molecule.

Aldehydes↗
PubMed1990

Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance.

The RNA of the Escherichia coli RNA phages is highly structured with 75% of the nucleotides estimated to take part in base-pairing. We have used enzymatic and chemical sensitivity of nucleotides, phylogenetic sequence comparison and the phenotypes of constructed mutants to develop a secondary structure model for the central region (900 nucleotides) of the group I phage MS2. The RNA folds into a number of, mostly irregular, helices and is further condensed by several long-distance interactions. There is substantial conservation of helices between the related groups I and II, attesting to the relevance of discrete RNA folding. In general, the secondary structure is thought to be needed to prevent annealing of plus and minus strand and to confer protection against RNase. Superimposed, however, are features required to regulate translation and replication. The MS2 RNA section studied here contains three translational start sites, as well as the binding sites for the coat protein and the replicase enzyme. Considering the density of helices along the RNA, it is not unexpected to find that all these sites lie in helical regions. This fact, however, does not mean that these sites are recognized as secondary structure elements by their interaction partners. This holds true only for the coat protein binding site. The other four sites function in the unfolded state and the stability of the helix in which they are contained serves to negatively control their accessibility. Mutations that stabilize helices containing ribosomal binding sites reduce their efficiency and vice versa. Comparison of homologous helices in different phage RNAs indicates that base substitutions have occurred in such a way that the thermodynamic stability of the helix is maintained. The evolution of individual helices shows several distinct size-reduction patterns. We have observed codon deletions from loop areas and shortening of hairpins by base-pair deletions from either the bottom, the middle or the top of stem structures. Evidence for the coaxial stacking of some helical segments is discussed.

Base Composition↗
PubMed1990

Repair of single nucleotide DNA mismatches transfected into mammalian cells can occur by short-patch excision.

Synthetic DNA linkers containing a single mismatched nucleotide (C:A) are repaired without bias at high efficiency when introduced into mammalian cells on a SV40 shuttle vector. From the pattern of repair in vectors containing multiple linkers, it appears that DNA synthesis following mismatch excision can replace a length of DNA as short as 40 nucleotides. Furthermore, results from the introduction of linker molecules containing combinations of single-strand nicks suggest that transient unsealed nicks do not drive the direction of mismatch repair in mammalian cells, as has previously been proposed.

Animals↗
PubMed2003

Interactions between Egr1 and AP1 factors in regulation of tyrosine hydroxylase transcription.

Several treatments which regulate tyrosine hydroxylase (TH) transcription, such as stress in vivo, or 12-O-tetradecanoylphorbol-13-acetate (TPA) in cell culture, induce both Egr1 and AP1 factors. Previously, we identified a functional Egr1 motif overlapping with Sp1 site in the rat TH promoter. Its response to Egr1 also required the presence of an AP1/Ebox motif. Here, we further examined the cross-talk between these sites. Insertion of 10- or 20-bp between the Sp1/Egr1 and AP1/Ebox elements, reduced the ability of Egr1 to upregulate luciferase reporter activity controlled by the proximal 272 nucleotides of the rat TH promoter in PC12 cells. Electrophoretic mobility shift assays with nuclear extracts from TPA treated cells were used to identify the composition of the factors which bound the AP1/Ebox motif and whether there is competition with factors which bind the Sp1/Egr1 motif. The complexes formed with labeled AP1/E box oligonucleotide were reduced or supershifted with antisera to Fos family, c-Fos, Fra-2, and Jun D. Excess Sp1/Egr1 oligonucleotide or anti Egr1 antisera did not compete. Fra-2 was a major component of the complex after 2-4 h TPA. Transfection of PC12 cells with Fra-2 induced reporter activity requiring the AP1, but not the Egr1 motif. However, when cotransfected with Fra-2, Egr1 expression plasmids elicited lower induction of luciferase activity than observed with Egr1 alone. Our results suggest that although it does not compete for binding to the promoter, Egr1 can modulate the regulation of TH transcription by AP1 factors.

Amino Acid Motifs↗