Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “oligonucleotide composition”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 883 records · Page 49Linked to original sources
PubMed1995

A short autocomplementary sequence in the 5' leader region is responsible for dimerization of MoMuLV genomic RNA.

Previous work has shown that a region of Moloney murine leukemia virus (MoMuLV) RNA located between nucleotides 280 and 330 in the PSI region (nt 215-565) is implicated in the dimerization process. We show with a deletion from nucleotides 290-299 in PSI RNA transcripts and through an antisense oligonucleotide complementary to nucleotides 275-291 that the 283-298 region is involved in RNA dimer formation in vitro. In an attempt to further characterize the mechanism of dimer formation, a series of short RNA transcripts was synthesized which overlapps the PSI region of MoMuLV RNA. The dimerization of these RNAs is temperature dependent. The predicted secondary structure of the 278-303 region, as a function of temperature, reveals that this sequence is able to adopt two conformations: (1) the U288 AGCUA293 sequence in a loop; (2) part of the same nucleotides implicated in a stem. These results, together with thermodynamic analysis, strongly suggest that (1) the loop conformation of the UAGCUA sequence modulates the relative amount of RNA dimer and (2) a 16 bp long Watson-Crick base pairing is involved in RNA dimer formation. We propose that loop-loop recognition via the U288 AGCUA293 sequence leads to a stable structure induced by a stem-loop opening. Furthermore, our results do not support purine quartet formation as necessary for the dimerization of the 5' leader MoMuLV RNA.

Base Composition↗
PubMed1990

Interaction of oligonucleotides containing 6-O-methylguanine with human DNA (cytosine-5-)-methyltransferase [published erratumm appears in Biochemistry 1992 Aug 4;31(30):7008].

Thirty-base-pair synthetic oligonucleotide duplexes containing a single meG.C (meG = 6-O-methylguanine) or A.C base pair at the 16th position (i.e., 5'-CCCGTTTAAATATACXTATACCCGGGTACC-3', where X = A or meG) were used to study de novo methylation by the purified human DNA (cytosine-5)-methyltransferase isolated from CEM cells. Both duplexes containing meG.C and A.C base pairs show enhanced methyl group acceptor properties. Subsequent introduction of hemimethylated sites at the 15th position of the top strand (the C residue next to the abnormal base pair) and the 7th, 15th (which represents the C residue in the 6meG.C and A.C base pairs), and 27th positions of the bottom strand were used to study the maintenance methylation of the hemimethylated duplexes by the methylase. This revealed striking differences in the rate, amount, and sites of methylation, which are dependent on the position of the hemimethylated site in the duplex. The possible mechanism of action of the methylase is discussed. The data show that 6-O-methylguanine residues in DNA can have other genetic effects apart from their miscoding behavior and that meG.C and A.C base pairs exert different effects in terms of methylation.

Base Composition↗
PubMed2002

Sequence diversity of Jeryl Lynn strain of mumps virus: quantitative mutant analysis for vaccine quality control.

The Jeryl Lynn strain of mumps vaccine live (MVL) was developed in 1966 by Merck Co. and has been widely used in the U.S. and other countries since the early 1970s. Partial sequencing has recently shown that the vaccine contains a mixture of two substrains with substantially different nucleotide sequences. We have determined the complete genomic sequences of both substrains and identified 414 nucleotide differences (2.69%), leading to 87 amino acid substitutions (1.67%). We used this information to develop methods for quantification of the substrain components in vaccine samples based on PCR and restriction enzyme cleavage and oligonucleotide microarray hybridization and monitored their dynamics in viral populations propagated in different conditions. Passaging Jeryl Lynn strain in Vero or CEF cell cultures resulted in rapid selection of the major component JL1, while growth in embryonated chicken eggs (ECE) favored accumulation of the minor component JL2. Based on the findings presented here, it is proposed that the substrain composition of Jeryl Lynn vaccine can be monitored as a part of its quality control to ensure consistency of the vaccine.

Amino Acid Sequence↗
PubMed1993

Single point mutation in human glycoprotein IIIa is associated with a new platelet-specific alloantigen (Mo) involved in neonatal alloimmune thrombocytopenia.

Here we describe a new platelet-specific alloantigen that was identified in a case of neonatal alloimmune thrombocytopenia. This antigen has provisionally been called "Mo." By studying the Mo family, it was shown to be inherited in an autosomal dominant manner. Immunoprecipitation and Western blot analysis showed that the antigen resides on platelet glycoprotein IIIa (GP IIIa). Genomic analysis, performed by applying polymerase chain reaction and sequencing, showed a C-->G substitution of base pair 1267 of the coding region of the DNA for GP IIIa, resulting in a substitution of Proline407 by Alanine407. That this substitution is associated with the antigen could be demonstrated by restriction fragment length polymorphism analysis of cDNA, prepared from platelet RNA, and of genomic DNA. It was confirmed by dot-blot hybridization with allele-specific oligonucleotides. All family members, also those being Mo antigen-positive, were healthy. None of them appeared to suffer from increased tendency of bleeding or thrombosis. Thus, the Mo mutation does not lead to significant platelet dysfunction in vivo with heterozygous carriers. One of 450 random healthy blood donors who were tested was positive for the Mo antigen. Typing was performed by the classical serologic methods as well as by DNA analysis.

Base Composition↗
PubMed1999

Phosphorothioate G3T4G3 motifs inhibits the early stage of HIV-1 infection.

It is well known that G-rich phosphorothioate oligonucleotides (G-rich PS) bind to the V3 loop of HIV-1 gp120 and inhibit HIV-1 infection. In this study, we investigated the inhibitory mechanism of a new type of G-rich PS (PS-G3T4G3) on the replication cycle of HIV-1. PS-G3T4G3 inhibits both cell to cell and cell free infections. Binding and entry assays revealed that the inhibitory step of PS-G3T4G3 occurs at the early stage of HIV-1 infection. V3 loop-specific mAb test showed that PS-G3T4G3 binds to the V3 loop and prevents its interaction with chemokine receptors. These results suggest that PS-G3T4G3 may be a novel candidate for an HIV-1 inhibitor.

Base Composition↗
PubMed1997

Antisense oligonucleotide binding to U5 snRNP induces a conformational change that exposes the conserved loop of U5 snRNA.

Conformational rearrangements of the spliceosomal small nuclear RNAs (U snRNAs) are essential for proper assembly of the active site prior to the first catalytic step of splicing. We have previously shown that conformational changes caused by binding of an antisense 2'-O-methyl RNA oligonucleotide (BU5Ae) to U5 snRNA nt 68-88 disrupted the U4/U5/U6 complex and induced formation of the U1/U4/U5 and U2/U6 complexes. Here we show that the conformational change induced by BU5Ae exposes the invariant loop of U5 that binds the 5'exon and also reorganizes internal loop 1 (IL1) and the top of stem 2. Interestingly, we have also previously found that the U1/U4/U5 complex induced by BU5Ae brings the invariant loop of U5 into close proximity with the 5'-end of U1. Taken together, these data suggest that U1 and U5 may both contribute to the ability of the U1/U4/U5 complex to bind the 5' splice site.

Base Composition↗
PubMed2002

Quantifying the impact of wastewater micronutrient composition on in situ growth activity of Acinetobacter spp.

Batch growth studies with pure cultures of Acinetobacter johnsoniiT and Acinetobacter johnsonii strain 210 on various media formulations were used to examine the effects of micronutrient composition on the growth rate of microbial populations in wastewater treatment systems. On nutrient rich Luria-Bertani medium, both strains of A. johnsonii grew with a doubling time of approximately 30 min. On a defined, minimal medium with acetate as the sole carbon source, the doubling time of A. johnsoniiT was 9.62 h and the doubling time of strain 210a was 2.6 h. Using a synthetic wastewater as a growth medium, the type strain had a doubling time of 56 h and strain 210a had a doubling time of 9.62 h. The concentration and redox state of iron appeared to be the principle growth limiting factors with higher doubling times occurring in media containing ferric iron as compared to ferrous iron. Additionally, grab samples from batch growth experiments were analyzed with oligonucleotide hybridization probes targeting the mature 16S ribosomal RNA (rRNA) and precursor 16S rRNA of Acinetobacter spp. Results showed that the precursor 16S rRNA levels responded more rapidly and to a greater extent than total 16S rRNA levels to changes in the micronutrient composition of the growth media. Precursor 16S rRNA levels increased in both strains when overnight cultures were diluted with fresh media and when micronutrient supplements were added to growing cultures. Our results show that the micronutrient composition of the influent wastewater can have a significant impact on the microbial community structure in wastewater treatment systems.

Acinetobacter↗
PubMed1994

Assignment of human satellite 1 DNA as revealed by fluorescent in situ hybridization with oligonucleotides.

We have used a fluorescent in situ hybridization procedure to detect human satellite 1 DNA, the simple sequence family that constitutes the non-male-specific fraction of classical satellite 1 DNA. Satellite 1 appears to be located on pericentromeric regions of chromosomes 3, 4 and 13, and on satellites of each acrocentric chromosome. These results suggest a possible relationship between quinacrine fluorescence of heterochromatin and DNA composition. Furthermore, by means of multicolour in situ hybridization, we have spatially resolved satellite 1 sequences and centromeric alpha-satellite within heterochromatic blocks.

Base Sequence↗
PubMed1992

NMR study of self-paired parallel duplex of d(AAAAACCCCC) in solution.

The oligonucleotide d(A5C5) in solution forms a parallel self-duplex at neutral and low pH values. H2O NMR spectra at pH 5.1 indicate the presence of five imino resonances at lower temperatures; and the structure is stable up to 60 degrees C. These signals can arise only from the hemiprotonated C+.C pairs [Westhof, E. and Sundaralingham, M. (1980) Biochemistry 77, 1852-1856; Westhof, E. and Sundaralingham, M. (1980) J. Mol. Biol. 142, 331-361] and constitute the first direct observation of C+.C hemiprotonated pairs in solution. The cross peaks from H1's and more than five distinct AH8's in 500 MHz 1H 2D-NOESY spectra indicate that there are two conformationally different and energetically similar A-tracts. There is good qualitative agreement between NOESY data and two theoretically derived structures in which A-tracts are reverse Watson-Crick and reverse Hoogsteen base-paired, respectively.

Base Composition↗
PubMed2002

A-tract DNA disfavours triplex formation.

Optimisation of DNA triplex stability is of fundamental importance in the anti-gene strategy. In the present work, thermal denaturation studies by UV-spectrophotometry and structural and dynamical characterizations by NMR spectroscopy have been used systematically to investigate the effects on triplex stability of isolated insertions of different base triplets into an otherwise homogeneous 15-mer dT x dA-dT oligo-triplex. It is found that insertion of a single central C(+) x G-C or T x D-T triplet (D=2,6-diaminopurine) leads to a pronounced stabilization (up to 20 deg. C if the cytosine base is C5 methylated) at acidic as well as neutral pH. To a smaller degree, this is the case also for a C(+) x I-C triplet insertion. Using imino proton exchange measurements, it is shown that insertion of a DT base-pair in the underlying duplex perturbs the intrinsic A-tract structure in the same way as has been shown for a GC insert. We propose that the intrinsic properties of A-tract duplex DNA (e. g. high propeller twist and rigidity) are unfavourable for triplex formation and that GC- or DT-inserts stabilize the triplex by interfering with the A-tract features of the underlying duplex. The C(+) x I-C triplet without the N2 amino group in the minor groove is readily accommodated within the typical, highly propeller-twisted A-tract structure. This might be related to its smaller effect on the stability of the corresponding triplex. These results may be valuable for understanding DNA triplex formation in vivo as well as for the design of efficient triplex-forming oligonucleotides and in choosing suitable target sequences in the anti-gene strategy.

Base Composition↗
PubMed2004

Inactivation of human adenovirus genome by different groups of disinfectants.

Human adenoviruses are model viruses for testing the virucidal efficacy of disinfectants. However, a recent study has shown that the chemical sensitivity of adenovirus serotypes varies significantly, possibly due to the composition of the viral capsid and/or the resistance of nucleic acids. We have investigated the effect of molecular changes in the viral genome of the human adenovirus subgenera C and D. A common oligonucleotide fragment within the hexon gene was amplified by polymerase chain reaction (PCR) after exposure to liposomal povidone-iodine (PVP-I), peracetic acid (PAA), and formaldehyde. The findings were compared with infectivity in cell cultures. PVP-I (0.125%) destroyed the infectivity of most serotypes within 60 min. However, PCR revealed no destruction of the adenoviral genome in most serotypes, even after exposure to higher PVP-I concentrations. PAA (0.5%) failed to inactivate the hexon gene of adenovirus types 22 and 44. Furthermore, the hexon gene of adenovirus type 22 was not altered by 0.7% formaldehyde. In conclusion, the genomes of human adenoviruses show considerably more chemical resistance than the complete viral particle. The molecular resistance of individual serotypes also varies. However, there was no clear correlation between the differences in the effect of disinfectants on infectivity of the complete viral particle and destruction of the viral genome.

Adenoviruses, Human↗
PubMed2003

Global analysis of gene expression using GeneChip microarrays.

DNA microarray technology, especially the use of GeneChip microarrays, has become a standard tool for parallel gene expression analysis. Recent improvements in GeneChip microarrays enable whole-genome expression analysis, and thus open a new avenue for studies of the composition, dynamics, and regulation of the transcriptome in plants.

Computational Biology↗
PubMed2000

The possible role of volcanic aquifers in prebiologic genesis of organic compounds and RNA.

In a volcanic aquifer, a wide range of physical and chemical conditions are not merely possible, but to be expected: relatively oxidizing and reducing environments both are present; hot and moderate temperatures can be expected; distillation and reflux conditions are probable to allow concentration of reactants, stimulation of reaction and fractionation of isotopes; apatite, hydroxides, clays and sulfide minerals are present to act as chromatographic media for separating compounds, to serve as catalytic surfaces and to provide potential energy sources; supersaturated precipitation of optically active crystals is reasonable, allowing for chromatographic separation of racemic mixtures by the resulting fixed chiral phase; and saturated and unsaturated conditions both are present for promotion of constructive reactions and inhibiting destructive hydrolysis reactions. Because the multitude of physical-chemical environments makes the setting robust with respect to circumventing commonly identified problems in origin-of-life theories, even if objections to details proposed herein are identified, the setting is favorable for devising alternatives. This paper describes a theory for the genesis of organic compounds, including RNA, in the mixing zone of juvenile and meteoric waters above a leaky semi-confined aquifer. Starting with basic reactants for best-guess conditions on Archean Earth, parallel sequences of specific reactions are proposed that culminate with RNA oligonucleotides, key molecules in contemporary life. All proposed reactions, or close analogues, are experimentally confirmed and all are set in plausible Archean conditions. Calculations indicate that the proposed reactions would yield C isotopic compositions that are consistent with observed biologic C.

Archaea↗
PubMed1997

Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution.

The crystal structure of a PNA duplex reveals both a right- and a left-handed helix in the unit cell. The helices are wide (28A), large pitched (18bp) with the base pairs perpendicular to the helix axis, thereby demonstrating that PNA besides adapting to oligonucleotide partners also has a unique structure by itself.

Base Composition↗
PubMed1995

Developmentally excised DNA sequences in Euplotes crassus capable of forming G quartets.

Tens of thousands of DNA segments are eliminated by DNA breakage and rejoining events during the formation of a new macronucleus in the hypotrichous ciliated protozoan Euplotes crassus. This study presents evidence for a class of eliminated sequences referred to as telomeric-repeat-like internal eliminated sequences (TelIESs). TelIESs are shorter (< 50 bp) than most previously characterized IESs and their DNA sequences resemble the telomeric repeat sequences of the organism. The TelIESs are excised during the developmental period of chromosome fragmentation/telomere addition, which is later than previously characterized IESs. Additional studies demonstrate that oligonucleotides representing the TelIESs are, like telomeric repeats, capable of forming G-quartet structures in vitro.

Animals↗
PubMed1995

Homology requirements for ligation and strand exchange by the FLP recombinase.

The FLP recombinase of the 2-microns plasmid of Saccharomyces cerevisiae belongs to the integrase family whose members form a covalent bond between a conserved tyrosine of the recombinase and the 3'-phosphoryl group at the site of cleavage. Ligation takes place when the 5'-OH generated during the cleavage step attacks the phosphotyrosine bond and reforms a phosphodiester bond. When the incoming 5'-OH is from the partner duplex, strand exchange occurs. The FLP recognition target (FRT) contains two inverted 13-base pair (bp) FLP binding sequences that surround an 8-bp core region. It has been shown that heterology in the core regions of the recombinase FLP recognition target sites can dramatically impair recombination. Therefore, it was of interest to study the homology requirements of the core sequence for FLP-mediated ligation. Using nicked duplex substrates containing mismatches in the core sequence, we have demonstrated that the FLP ligation reaction can tolerate mismatches at all positions in the 8-bp core except the position immediately adjacent to the cleavage site. Using half-FRT substrates that contain a single-stranded core sequence, we showed that 4 base pairs adjacent to the cleavage site in the core are required for FLP to execute ligation with a single-stranded oligonucleotide. FLP is also able to ligate the protruding single strand on a half-FRT site to the opposite strand to form a hairpin. We have studied the effect of the base composition of the protruding 8-nucleotide single strand upon the efficiency of hairpin ligation. These studies revealed the importance of intrastrand complementarity in the formation of hairpin by FLP. Hence we conclude that the homology in the position adjacent to the cleavage site is most important, and the degree of the homology required is dependent on the nature of the ligation assay.

Base Composition↗
PubMed2000

The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex.

The sliding clamp model of transcription processivity, based on extensive studies of Escherichia coli RNA polymerase, suggests that formation of a stable elongation complex requires two distinct nucleic acid components: an 8-9-nt transcript-template hybrid, and a DNA duplex immediately downstream from the hybrid. Here, we address the minimal composition of the processive elongation complex in the eukaryotes by developing a method for promoter-independent assembly of functional elongation complex of S. cerevisiae RNA polymerase II from synthetic DNA and RNA oligonucleotides. We show that only one of the nucleic acid components, the 8-nt RNA:DNA hybrid, is necessary for the formation of a stable elongation complex with RNA polymerase II. The double-strand DNA upstream and downstream of the hybrid does not affect stability of the elongation complex. This finding reveals a significant difference in processivity determinants of RNA polymerase II and E. coli RNA polymerase. In addition, using the imperfect RNA:DNA hybrid disturbed by the mismatches in the RNA, we show that nontemplate DNA strand may reduce the elongation complex stability via the reduction of the RNA:DNA hybrid length. The structure of a "minimal stable" elongation complex suggests a key role of the RNA:DNA hybrid in RNA polymerase II processivity.

Amino Acid Sequence↗