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Synthetic Oligonucleotides (synthetic + oligonucleotide)
Selected AbstractsPhotocrosslinking in Ruthenium-Labelled Duplex OligonucleotidesCHEMBIOCHEM, Issue 2-3 2003O. Lentzen Abstract The formation of a photoadduct between a [Ru(1,4,5,8-tetraazaphenanthrene)24,7-diphenylphenanthroline]2+complex chemically attached to a synthetic oligonucleotide, and a guanine moiety in a complementary targeted single-stranded DNA molecule was studied for ten 17-mer duplexes by denaturing gel electrophoresis. This photoadduct formation leads to photocrosslinking of the two strands. The percentage quenching of luminescence of the complex by electron transfer was compared to the resulting yield of photocrosslinked product. This yield does not only depend on the ionisation potential of the guanine bases, which are electron donors, but also on other factors, such as the position of the guanine bases as compared to the site of attachment of the complex. The photocrosslinking yield is higher when the guanine moieties are towards the 3, end on the complementary strand as compared to the tethering site. Computer modelling results are in agreement with this preference for the 3, side for the photoreaction. Interestingly, the photocrosslink is not alkali labile. Moreover, a type III exonuclease enzyme is blocked at the position of photocrosslinking. [source] Alu-DNA repeat-binding protein p68 is a part of Alu-RNA containing ,-RNPFEBS JOURNAL, Issue 8 2000Dmitry V. Lukyanov An Alu-DNA repeat-binding protein with a molecular mass of 68 kDa (p68) is identified in the somatic human cell nucleoplasm. Gel mobility shift assay (GMSA), South-western blotting and affinity purification on DNA attached to the carrier were used in the identification. GMSA revealed multiple complexes with the exponential dependence of their relative mobility. A narrow binding site of the p68 was revealed using synthetic oligonucleotides. It is located between the A-box and B-box of the RNA polymerase III promoter and is identical to that reported for the Alu-binding protein from human spermatozoids. The same narrow binding site, the similarity of the isolation procedure from germ and somatic cells, and similar binding properties and molecular masses suggest homology of the two proteins. Antibodies raised against Alu-protein complexes led to hypershift of the complexes in GMSA and stained p68 in active fractions in human spermatozoids and in Alu-RNA-containing ,-RNP particles. Immunofluorescence of a HeLa cell monolayer revealed an intranuclear dot pattern with the dots corresponding to euchromatin areas and some dots located at the cell periphery in the cytoplasm. ,-RNP particles bound Alu-DNA in vitro and contained p68 as shown using the immunogold procedure. Alu-DNA binding activity was revealed in cytoplasm as well as in nucleoplasm. The possible nature of the main Alu-DNA binding protein and its involvement in the particle structure are discussed. [source] Controlled size chitosan nanoparticles as an efficient, biocompatible oligonucleotides delivery systemJOURNAL OF APPLIED POLYMER SCIENCE, Issue 4 2010Romila Manchanda Abstract Polymeric nanoparticles of chitosan crosslinked with glutaraldehyde have been prepared using reverse micellar system. An optically clear solution was obtained on redispersing these nanoparticles in aqueous buffer. The nanoparticles were characterized for their size and surface morphology employing dynamic laser scattering (DLS) and transmission electron microscopy (TEM). The TEM images showed spherical particles with smooth surface and narrow size distribution of about 90 nm, which was also supported by DLS data. Size and morphology of the particles remains the same on redispersing the lyophilized powder of these nanoparticles in aqueous buffer. Further, these nanoparticles were loaded with different synthetic oligonucleotides (ODNs). In vitro pH dependent release of the adsorbed oligonucleotides from these nanoparticles was also studied. At basic pH the release of oligonucleotides was found higher as compared with neutral and acidic medium. Cytotoxicity studies done on HEK 293 cells reveals that oligonucleotide loaded nanoparticles have high cell viability of nearly 76,88% whereas those of lipofectamine was about 35%. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010 [source] Mechanism of DNA Damage Photosensitized by Trisbipyrazyl Ruthenium Complex.PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 5 2000Unusual Role of Cu/Zn Superoxide Dismutase ABSTRACT Trisbipyrazyl ruthenium(II) (Ru[bpz]32+) was examined as DNA photosensitizer. Damage resulting from the photolysis of synthetic oligonucleotides has been monitored by polyacrylamide gel electrophoresis. Photoadduct formation is found on both single- and double-stranded oligonucleotides. On oligonucleotide duplex, oxidative damage occurs selectively at the 5,G of the 5,GG3, site and to a lesser extent at the 5,G of a GA sequence. These findings suggest the involvement of electron transfer and show that this mechanism is the main DNA damaging process involved in Ru(bpz)32+ photosensitization. In addition, photoadducts and oxidative damage are both highly affected by an increase of salt concentration in the reaction medium, stressing the importance of direct interactions between nucleic acid bases and the excited ruthenium complex for efficient electron transfer. On single-stranded oligonucleotides, all the guanines are oxidized to the same extent. In this case, oxidative damage, which is not affected by an increase of salt in the solution, has been attributed, in part, to singlet oxygen. More importantly, Cu/Zn superoxide dismutase (SOD) strongly enhances the yield of all damage, correlated to an increase of both electron transfer and singlet oxygen production. This original activity of SOD is the first example of bioactivation of a polyazaaromatic ruthenium complex. [source] De novo synthesis and assembly of multiplex riboswitches in vitroBIOTECHNOLOGY PROGRESS, Issue 5 2009Hao-Hua Sun Abstract Pools of short synthetic oligonucleotides (oligos) are required in the multiplex and parallel DNA construction. Microarray technology provides a fast and economical mean for massive parallel synthesis of oligos. The method of oligo synthesis with the programmable microfluidic PicoArray could simultaneously synthesize the designed oligos for multiple riboswitch genes. The synthetic oligos were recovered and purified as a pool of oligo mixture (OligoMix). Three temperature steps were employed to denature, anneal and extend the designed OligoMix until, after multiple rounds of thermocycling, the riboswitches with the desired length are obtained. The OligoMix was amplified using this PCR-based technique and the flanking adapter segments were cleaved for following assembly. Based on these oligos derived from 197 riboswitch sequences, the method of simultaneous assembling multiplex riboswitches (SAMRs) showed high fidelity by sequence identification. The resultant error rate was determined to be 2.78,. With the templates from SAMRs, in vitro transcription was applied to produce milligram amounts of biologically active riboswitches. With the verification of biological activity based on the high specificity of recognizing small-molecule metabolites as well as the DNA sequence redivivus by RT-PCR, the assembled riboswitches can be used for further gene operation and biological application. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Expression and function of Toll-like receptor 9 in severely injured patients prone to sepsisCLINICAL & EXPERIMENTAL IMMUNOLOGY, Issue 3 2006E. E. Baiyee Summary The purpose of this prospective study was to enumerate Toll-like receptor 9 (TLR9)+ cells and measure their function using synthetic oligonucleotides enriched in CG dinucleotide motifs (CpG)-induced proliferation within 48 h after trauma in severely injured patients prone to sepsis. Sixteen consecutive trauma patients with an injury severity score (ISS) > 21 and 16 blood donors (controls) were included in this study. Using two-colour flow cytometry, TLR9 expression was detectable intracellularly and also on the surface of B lymphocytes. The surface expression of TLR9 of B lymphocytes from whole blood and peripheral blood mononuclear cells (PBMC) stimulated with CpG was significantly increased in B cells of severely injured patients prone to sepsis compared to controls. No significant differences could be observed between CpG-induced proliferation of PBMC of severely injured patients prone to sepsis and controls. As a measure of immunosuppression, human leucocyte antigen (HLA)-DR expression of monocytes of the trauma patients was significantly diminished compared with controls in PBMC and in whole blood. Immunosuppression in the early phase after trauma seems not to be associated with a disturbed sensing of bacterial DNA. [source] | |||||||||||||