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Nucleosides, Nucleotides & Nucleic Acids

Erkan Halay, Emriye Ay, Emine Şalva, Kadir Ay, Tamer Karayıldırım
With the aim to create a library of compounds with potential bioactivities by combining special characteristics of two important groups such as nucleobases and carbohydrates, twenty 1,4-disubstituted-triazole nucleosides were synthesized in good yields (80-94%) using the copper catalyzed 'Click' reaction between azido-modified pento- or hexopyranoses and alkyne-bearing pyrimidine or purine nucleobases. Structural elucidation was made with the assistance of spectroscopic techniques such as FTIR, 1D-, 2D-NMR, and ESI-TOFMS...
September 2, 2017: Nucleosides, Nucleotides & Nucleic Acids
Michelle E Whittum, Joshua M Blose
Osmolytes have the potential to affect the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in the cell. To contribute to the understanding of the in vivo function of RNA we observed the effects of different classes of osmolytes on the UNCG tetraloop motif. UNCG tetraloops are the most common and stable of the RNA tetraloops and are nucleation sites for RNA folding. They also have a significant thermodynamic preference for a CG closing base pair. The thermal denaturation of model hairpins containing UUCG loops was monitored using UV-Vis spectroscopy in the presence of osmolytes with different chemical properties...
September 2, 2017: Nucleosides, Nucleotides & Nucleic Acids
Cobra Izanloo
An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ∼1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule...
September 2, 2017: Nucleosides, Nucleotides & Nucleic Acids
Neda Hosseinpour Moghadam, Sadegh Salehzadeh, Nahid Shahabadi
The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations...
September 2, 2017: Nucleosides, Nucleotides & Nucleic Acids
Surender Kumar, Sukhvinder, Vinod Kumar, Girish Kumar Gupta, Vikas Beniwal, Fatma Abdmouleh, Emna Ketata, Mehdi El Arbi
In order to explore the biological potential, some synthesized triazolylnucleosides were evaluated for their antibacterial, tyrosinase and DNA photocleavage activities. Triazolylnucleosides (5-12) were screened against Staphylococcus aureus (ATCC 6538), gram-positive and Escherichia coli (ATCC 10536), gram-negative bacterial strains. Among the series, compound 9 exhibited a significant level of antibacterial activity against both strains at higher concentration in reference to the standard drug, Levofloxacin...
August 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Nahid Shahabadi, Mohammad Hakimi, Teimoor Morovati, Navid Fatahi
The interaction of a novel macrocyclic copper(II) complex, ([CuL(ClO4)2] that L is 1,3,6,10,12,15-hexaazatricyclo[,10)]eicosane) with calf thymus DNA (ct-DNA) was investigated by various physicochemical techniques and molecular docking at simulated physiological conditions (pH = 7.4). The absorption spectra of the Cu(II) complex with ct-DNA showed a marked hyperchroism with 10 nm blue shift. The intrinsic binding constant (Kb) was determined as 1.25 × 10(4) M(-1), which is more in keeping with the groove binding with DNA...
August 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Hena Paul, Buddhadeb Sen, Tapan Kumar Mondal, Pabitra Chattopadhyay
Two new ruthenium(II) complexes of Schiff base ligands (L) derived from cinnamaldehyde and ethylenediamine formulated as [Ru(L)(bpy)2](ClO4)2, where L(1) = N,N'-bis(4-nitrocinnamald-ehyde)ethylenediamine and L(2) = N,N'-bis(2-nitrocinnamaldehyde)-ethylenediamine for complex 1 and 2, respectively, were isolated in pure form. The complexes were characterized by physicochemical and spectroscopic methods. The electrochemical behavior of the complexes showed the Ru(III)/Ru(II) couple at different potentials with quasi-reversible voltammograms...
August 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Galal H Elgemeie, Mamdouh A Abu-Zaied
A novel synthesis of thiophene thioglycosides is carried out via a one-pot reaction of sodium thiophenethiolates with α-halogeno sugars. The sodium thiophenethiolate salts were prepared using sodium cyanoethylene thiolate salts. The structures of the reaction products were established on the basis of their elemental analysis and spectral data (IR, (1)H NMR, MS, and (13)C NMR).
August 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Wael A El-Sayed, Walaa I El-Sofany, Hoda A R Hussein, Nahed M Fathy
New [(Indolyl)pyrazolyl]-1,3,4-oxadiazole compounds and their derived thioglycosides as well as the corresponding sugar hydrazones were synthesized. The acyclo C-nucleoside analogs of the oxadiazoline base system were also prepared by reaction of acid hydrazides with aldehydo sugars followed by one pot process encompassing acetylation and cyclization of the synthesized hydrazones. The anticancer activity of the newly synthesized compounds was studied against colorectal carcinoma (HCT116), breast adenocarcinoma (MCF7) and prostate cancer (PC3) human tumor cell lines and a number of compounds showed moderate to high activities...
July 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Hiroki Kumamoto, Misato Fukano, Shuhei Imoto, Satoru Kohgo, Yuki Odanaka, Masayuki Amano, Nobuyo Kuwata-Higashi, Hiroaki Mitsuya, Kazuhiro Haraguchi, Kiyoshi Fukuhara
Synthesis of a novel 2'-deoxy-guanine carbocyclic nucleoside 4 constructed with spiro[2.4]heptane core structure in the aglycon moiety was carried out. Radical-mediated 5-exo-dig mode cyclization and following cyclopropanation proceeded efficiently to furnish the spiro alcohol 10. Subsequent Mitsunobu-type glycosylation between 13 and 14, deoxygenation of the 2'-hydroxyl group of 16 and deprotection of 17 gave the title compound 4. Compound 4 demonstrated moderate anti-HBV activity (EC50 value of 0.12 ± 0...
July 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Neda Hosseinpour Moghadam, Sadegh Salehzadeh, Nahid Shahabadi, Reza Golbedaghi
The possible interaction between the antiviral drug oseltamivir and calf thymus DNA at physiological pH was studied by spectrophotometry, competitive spectrofluorimetry, differential pulse voltammogram (DPV), circular dichroism spectroscopy (CD), viscosity measurements, salt effect, and computational studies. Intercalation of oseltamivir between the base pairs of DNA was shown by a sharp increase in specific viscosity of DNA and a decrease of the peak current and a positive shift in differential pulse voltammogram...
July 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Khue Vu Nguyen, Sebastian Silva, Monica Troncoso, Robert K Naviaux, William L Nyhan
Lesch-Nyhan disease (LND) is a rare X-linked inherited neurogenetic disorder of purine metabolism in which the enzyme, hypoxanthine-guanine phosphoribosyltransferase (HGprt) is defective. The authors report two independent point mutations leading to splicing errors: IVS 2 +1G>A, c.134 +1G>A, and IVS 3 +1G>A, c.318 +1G>A in the hypoxanthine-phosphoribosyltransferase1 (HPRT1) gene which result in exclusion of exon 2 and exon 3 respectively, in the HGprt enzyme protein from different members of two Chiloé Island families...
July 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Olga V Kirsanova, Alexander V Sergeev, Ivan S Yasko, Elizaveta S Gromova
The incorporation of chemotherapeutic agent 6-thioguanine ((S)G) into DNA is a prerequisite for its cytotoxic action. This modification of DNA impedes the activity of enzymes involved in DNA repair and replication. Here, using hemimethylated DNA substrates we demonstrated that DNA methylation by Dnmt3a-CD is reduced if DNA is damaged by the incorporation of (S)G into one or two CpG sites separated by nine base pairs. An increase in the number of (S)G substitutions did not enhance the effect. Dnmt3a-CD binding to either of (S)G-containing DNA substrates was not distorted...
June 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Tetsuya Suzuki, Takashi Imada, Yasuo Komatsu, Hiroyuki Kamiya
Pinpoint sequence alteration (genome editing) by the combination of the site-specific cleavage of a target DNA and a donor nucleic acid has attracted much attention and the sequence of the target DNA is expected to be changed to that of a donor nucleic acid. In most cases, oligodeoxyribonucleotides (ODNs) and plasmid DNAs have been used as donors. However, a several hundred-base single-stranded (ss) DNA fragment and a 5'-tailed duplex (TD) accomplished the desired sequence changes without DNA cleavage, and might serve as better donors for the cleaved target DNA than ODNs and plasmid DNAs...
June 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Vladimir A Ryabinin, Elena V Kostina, Alexander N Sinyakov
The fluorescence quenchers BHQ1 and BHQ2 can be modified by trace amounts of ammonium persulfate, used for initiating gel polymerization, in electrophoretic purification of TaqMan probes using a denaturing polyacrylamide gel. The case study of BHQ1 quencher has demonstrated that a Boyland-Sims reaction proceeds in the presence of ammonium persulfate to give the corresponding sulfate. The absorption maximum of the resulting quencher shifts to the short-wavelength region relative to the absorption maximum of the initial BHQ1...
June 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
April Maschmann, Kristy L Kounovsky-Shafer
Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously...
June 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
Denise J Trans, Ruoli Bai, J Bennet Addison, Ruiwu Liu, Ernest Hamel, Matthew A Coleman, Paul T Henderson
Fluorescent GTP analogues are utilized for an assortment of nucleic acid and protein characterization studies. Non-hydrolysable analogues such as GTPγS offer the advantage of keeping proteins in a GTP-bound conformation due to their resistance to hydrolysis into GDP. Two novel fluorescent GTPγS molecules were developed by linking fluorescein and tetramethylrhodamine to the γ-thiophosphate of GTPγS. Chemical and biological analysis of these two compounds revealed their successful synthesis and ability to bind to the nucleotide-binding site of tubulin...
June 3, 2017: Nucleosides, Nucleotides & Nucleic Acids
S Karthik, A Thirugnanasambandam, P K Mandal, N Gautham
We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)2 all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions...
May 4, 2017: Nucleosides, Nucleotides & Nucleic Acids
Galal H Elgemeie, Nahed M Fathy, Ayman B Farag, Sheikha A Alkursani
A convenient synthesis of a novel series of dihydropyridine and pyridine thioglycosides was developed. The evaluation of anti-proliferative activity against HepG-2 cell lines (liver carcinoma cell lines) shows that most of the compounds have antitumor activity, especially 5b, 5f, 5j, 5n, 7b, 7f, 7j, 7n, 8b, 8f, and 8j. The results of molecular docking reveal that these compounds have high binding affinity by hydrogen bond formation with the binding pocket of thymidylate synthase dihydrofolate reductase (TS-DHFR)...
May 4, 2017: Nucleosides, Nucleotides & Nucleic Acids
Galal H Elgemeie, Ayman B Farag
A first reported direct method for preparation of thymine thioglycoside analogs utilizing novel pyrimidine-2(1H)-thiones and α-bromoglucose or α-bromogalactose tetraacetate as starting components is described. The synthetic potential of the method is demonstrated. The evaluation of antiproliferative activity against HepG-2 cell lines (Liver carcinoma cell lines) shows that most of the compounds have high antitumor activities especially 6b, 6e, 11b, and 12b. Moreover, molecular modelings of these compounds reveal that they have high binding affinity through hydrogen bond interaction with the binding pocket of thymidylate synthase dihydrofolate reductase (TS-DHFR)...
May 4, 2017: Nucleosides, Nucleotides & Nucleic Acids
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