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European Journal of Biochemistry Jul 1970
Topics: Chemical Phenomena; Chemistry; Circular Dichroism; Cytosine Nucleotides; Dialysis; Guanine Nucleotides; Hydrogen-Ion Concentration; Optical Rotatory Dispersion; Osmolar Concentration; Polynucleotides; Potentiometry; Spectrophotometry
PubMed: 5472867
DOI: 10.1111/j.1432-1033.1970.tb00305.x -
Bioorganic Chemistry Jun 2003Schizophyllan belongs to a beta-1,3-D-glucan family, which exists as a random coil in dimethyl sulfoxide (DMSO) and as a triple helix in water, respectively. The...
Schizophyllan belongs to a beta-1,3-D-glucan family, which exists as a random coil in dimethyl sulfoxide (DMSO) and as a triple helix in water, respectively. The schizophyllan single chain forms a complex with single-stranded homo RNAs in water/DMSO mixed solvents. Using circular dichroism, we studied the complexation and its stability as a function of apparent pH (pH(*)) in a mixed solvent system and as a function of the salt concentration. The complex is formed in the pH(*) range 6.5-10, and dissociated in the pH(*) range 4-6. Both poly(A) and poly(C) adopt a double strand in the pH(*) range 4-6 and a single strand in the pH(*) range 6.5-10. Therefore, the conformational change of each polynucleotide is responsible for dissociation/association of the complex, i.e., the single strand of the polynucleotides can form complexes, whereas the double one cannot. This result indicates that hydrogen bonding and similarity of the helix parameters are essential for the complex formation. The melting temperature of the complex reaches the maximum around 0.05 M of NaCl and KCl, and the value of the maximum temperature depends on the cation species.
Topics: Circular Dichroism; Cytosine; Hydrogen Bonding; Hydrogen-Ion Concentration; Polynucleotides; Polysaccharides; Potassium Chloride; RNA; Sizofiran; Sodium Chloride; Transition Temperature
PubMed: 12818231
DOI: 10.1016/s0045-2068(03)00034-8 -
International Journal of Molecular... Jul 2023Osteoarthritis (OA) is characterized by degeneration of the joint cartilage, inflammation, and a change in the chondrocyte phenotype. Inflammation also promotes cell...
Osteoarthritis (OA) is characterized by degeneration of the joint cartilage, inflammation, and a change in the chondrocyte phenotype. Inflammation also promotes cell hypertrophy in human articular chondrocytes (HC-a) by activating the NF-κB pathway. Chondrocyte hypertrophy and inflammation promote extracellular matrix degradation (ECM). Chondrocytes depend on Smad signaling to control and regulate cell hypertrophy as well as to maintain the ECM. The involvement of these two pathways is crucial for preserving the homeostasis of articular cartilage. In recent years, Polynucleotides Highly Purified Technology (PN-HPT) has emerged as a promising area of research for the treatment of OA. PN-HPT involves the use of polynucleotide-based agents with controlled natural origins and high purification levels. In this study, we focused on evaluating the efficacy of a specific polynucleotide sodium agent, known as CONJURAN, which is derived from fish sperm. Polynucleotides (PN), which are physiologically present in the matrix and function as water-soluble nucleic acids with a gel-like property, have been used to treat patients with OA. However, the specific mechanisms underlying the effect remain unclear. Therefore, we investigated the effect of PN in an OA cell model in which HC-a cells were stimulated with interleukin-1β (IL-1β) with or without PN treatment. The CCK-8 assay was used to assess the cytotoxic effects of PN. Furthermore, the enzyme-linked immunosorbent assay was utilized to detect MMP13 levels, and the nitric oxide assay was utilized to determine the effect of PN on inflammation. The anti-inflammatory effects of PN and related mechanisms were investigated using quantitative PCR, Western blot analysis, and immunofluorescence to examine and analyze relative markers. PN inhibited IL-1β induced destruction of genes and proteins by downregulating the expression of MMP3, MMP13, iNOS, and COX-2 while increasing the expression of aggrecan (ACAN) and collagen II (COL2A1). This study demonstrates, for the first time, that PN exerted anti-inflammatory effects by partially inhibiting the NF-κB pathway and increasing the Smad2/3 pathway. Based on our findings, PN can potentially serve as a treatment for OA.
Topics: Animals; Humans; Male; NF-kappa B; Matrix Metalloproteinase 13; Polynucleotides; Cells, Cultured; Semen; Inflammation; Osteoarthritis; Chondrocytes; Anti-Inflammatory Agents; Hypertrophy; Interleukin-1beta
PubMed: 37569659
DOI: 10.3390/ijms241512282 -
Clinical Immunology and Immunopathology Aug 1986Three IgM monoclonal anti-DNA antibodies were produced by hybridoma techniques from an MRL-lpr/lpr mouse using denatured DNA (dDNA) as the selection antigen. All three...
Three IgM monoclonal anti-DNA antibodies were produced by hybridoma techniques from an MRL-lpr/lpr mouse using denatured DNA (dDNA) as the selection antigen. All three antibodies also bound poly(dT), poly(rA), and the single-stranded random copolymer poly(dI,dT), and each antibody displayed a unique preference for a limited array of other ribo- and deoxyribopolynucleotides based on direct binding as well as inhibition studies. Inability to identify a common primary structure in the polynucleotides reactive with each antibody suggested that higher ordered structures may be important. This notion was supported by the finding that oligomers of thymidine of 25-30 nucleotides or less were ineffective in blocking antibody binding to dDNA or poly(dT). However, deliberate destabilization of putative secondary structures by decreasing counterion concentration and increasing temperature had little effect on antibody binding to poly(dT). Since the antigenic polynucleotides in general contain little known secondary structure and considerable flexibility, antibody binding may be accompanied by local conformational changes in the polynucleotide that result in a better fit to the antibody combining site.
Topics: Animals; Antibodies, Antinuclear; Antibodies, Monoclonal; Antibody Specificity; Antigen-Antibody Reactions; Binding, Competitive; DNA; Female; Immunoglobulin M; Mice; Osmolar Concentration; Polynucleotides; Temperature
PubMed: 3487402
DOI: 10.1016/0090-1229(86)90022-x -
Proceedings of the National Academy of... Jun 1961
Topics: DNA; Polynucleotides; Protein Structure, Secondary
PubMed: 13770642
DOI: 10.1073/pnas.47.6.791 -
The Journal of Laboratory and Clinical... Feb 1986Antibodies to polynucleotides are seen primarily in systemic lupus erythematosus (SLE), but also occur in a variety of other connective tissue diseases. We looked at the...
Antibodies to polynucleotides are seen primarily in systemic lupus erythematosus (SLE), but also occur in a variety of other connective tissue diseases. We looked at the prevalence of antinucleotide antibodies (double- and single-stranded RNA and DNA [dRNA, sRNA, dDNA, and sDNA]) in the sera of patients with SLE (70), rheumatoid arthritis (RA) (31), juvenile rheumatoid arthritis (JRA) (68), osteoarthritis (12), and of 22 patients with a preceding viral illness. In comparison with sera from a control population, elevated mean antibody levels to sRNA were found in the sera of all the patients with connective tissue disease, as well as in the sera of patients with preceding RNA, but not DNA, viral infections. Elevated mean levels of antibodies to dRNA were seen in all groups with the exception of RA. Elevated mean antibody titers to sDNA were not seen in patients with JRA nor were they present in the sera of patients with preceding RNA viral infections. Elevated mean anti-dDNA titers were seen only in sera from patients with SLE. High correlation coefficients between the levels of antibodies to sRNA and dRNA in sera from SLE and RA, and between sDNA and dDNA in sera from SLE suggest cross-reactivity of the antibodies in these diseases. Immunization of an elderly population with influenza (RNA) viral vaccine induced antibodies to sRNA only. These studies further document the prevalence of antipolynucleotide antibodies in the sera of patients with connective tissue diseases.(ABSTRACT TRUNCATED AT 250 WORDS)
Topics: Adult; Age Factors; Aged; Antibodies; Connective Tissue Diseases; Cross Reactions; DNA; DNA, Single-Stranded; Humans; Influenza Vaccines; Middle Aged; Poly A; Poly A-U; Polynucleotides; RNA; RNA, Double-Stranded; Regression Analysis; Virus Diseases
PubMed: 2418139
DOI: No ID Found -
Science (New York, N.Y.) Jan 1973At 4 A resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 A apart. These peaks are probably...
At 4 A resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 A apart. These peaks are probably associated with the phosphate groups, while lower levels of electron density between segments of adjacent polynucleotide chains are interpreted as arising from hydrogen-bonded purine-pyrimidine base pairs. It is possible to trace the entire polynucleotide chain with only two minor regions of ambiguity. The polynucleotide chain has a secondary structure consistent with the cloverleaf conformation; however, its folding is different from that proposed in any model. The molecule is made of two double-stranded helical regions oriented at right angles to each other in the shape of an L. One end of the L has the CCA acceptor; the anticodon loop is at the other end, and the dihydrouridine and TpsiC loops form the corner.
Topics: Base Sequence; Models, Structural; Nucleic Acid Conformation; Phenylalanine; Polynucleotides; RNA, Transfer; Saccharomyces cerevisiae; X-Ray Diffraction
PubMed: 4566654
DOI: 10.1126/science.179.4070.285 -
Journal of Molecular Recognition : JMR Oct 2014Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of...
Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to fabricate high-throughput systems capable to fulfill the task in an efficient manner. Here, voltage gating OmpF nanochannel, whose structure is known at an atomic level, was used to recognize and differentiate between polynucleotide primers through voltage clamp technique. Our results showed that poly(T) occasionally blocked the channel at both polarities, while poly(C) and poly(G) obstructed it only at positive polarity. The channel was blocked at potential differences of as low as 80 mV in the presence of poly(T). The conductance of channel decreased in the presence of poly(C) and poly(G) by 61 and 5% respectively. Analysis of the number of events showed that poly(T) caused more closing events at higher voltages, while poly(G) and poly(C) induced it at lower voltages. Application of the hazard function as a statistical parameter and analysis of event closing times in various voltages demonstrated the most efficient differentiation at 60 mV. The results of practical and theoretical approaches presented here show that OmpF porin channel possesses the structural and dynamic characteristics required to be considered as a biosensor capable for continuous polynucleotide sequencing.
Topics: Genome, Human; Humans; Models, Molecular; Patch-Clamp Techniques; Poly C; Poly G; Poly T; Polynucleotides; Porins; Sequence Analysis, DNA
PubMed: 25178853
DOI: 10.1002/jmr.2381 -
Biochimica Et Biophysica Acta Apr 1965
Topics: Alkylation; Chemical Phenomena; Chemistry; Polynucleotides; Research
PubMed: 14324822
DOI: 10.1016/0005-2787(65)90525-3 -
European Journal of Biochemistry Aug 1989The proteolysis of the LexA repressor in the presence of RecA and various polynucleotides was studied by measuring the fluorescence decrease of LexA upon cleavage. The...
The proteolysis of the LexA repressor in the presence of RecA and various polynucleotides was studied by measuring the fluorescence decrease of LexA upon cleavage. The results were compared with the DNA binding of RecA to investigate the presence of multiple DNA-RecA complexes. All single-stranded polydeoxyribonucleotides (DNA) efficiently stimulated the proteolysis and the maximum activation was reached in the presence of three or four nucleotides of polynucleotide per monomer of RecA. The stimulative effect was decreased in the presence of larger amounts of poly(dA), poly(dT) or heat-denatured DNA, whereas the excess of single-stranded DNAs chemically modified with chloroacetaldehyde did not present such an inhibitory effect, despite the fact that a second DNA molecule is likely to interact with RecA as monitored by the intrinsic fluorescence of these DNA species. The complicated cleavage promotion and inhibition pattern is tentatively explained by a three-state model assuming that RecA may interact with three single-stranded DNA molecules. According to this model, occupation of the first site would be necessary and sufficient for cleavage promotion, the second site would be neutral with respect to cleavage and the occupation of the third site would inhibit LexA cleavage at least partially. Double-stranded natural DNA did not stimulate cleavage, even under conditions where RecA binds quantitatively to the DNA. No polyribonucleotides (RNA) examined showed a significant stimulative effect either, nor did they appear to interact with RecA.
Topics: Bacterial Proteins; DNA; Kinetics; Polynucleotides; Protein Binding; Rec A Recombinases; Repressor Proteins; Serine Endopeptidases; Transcription Factors
PubMed: 2776755
DOI: 10.1111/j.1432-1033.1989.tb21091.x