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Nucleosides, Nucleotides & Nucleic Acids

Yoshikazu Hattori, Daichi Yamanaka, Saori Morioka, Taishi Yamaguchi, Honoka Tomonari, Chojiro Kojima, Yoshiyuki Tanaka
Hammerhead ribozymes are a model system for studying molecular mechanism of RNA catalysis. Physicochemical data-driven mechanistic studies are an indispensable step towards understanding the catalysis of hammerhead ribozymes. Here we characterized a model RNA duplex with catalytically important sheared-type G12-A9 base pair and A9-G10.1 metal ion-binding motif in hammerhead ribozymes. By using high magnetic field NMR, all base proton signals, including catalytic residues, were unambiguously assigned. We further characterized structural features of this RNA molecule and found that it reflects the structural features of the A9-G10...
June 28, 2018: Nucleosides, Nucleotides & Nucleic Acids
H Kano, N Yamada, C Saito, Y Murayama-Chiba, Y Asami, H Ito
Lactobacillus gasseri PA-3 (PA-3) is a bacterial strain with a strong ability to degrade purine nucleosides. We previously showed that PA-3 incorporates purines in vitro and that oral administration of PA-3 and purines to rats attenuated their absorption of purines. It remains unclear whether these effects of PA-3 depend on bacterial strains. This study therefore compared the abilities of PA-3 and another bacterial strain of L. gasseri, OLL2996, which has shown decreased ability to degrade purine nucleosides in vitro, to incorporate purine nucleosides and to inhibit the absorption of purines fed to rats...
May 29, 2018: Nucleosides, Nucleotides & Nucleic Acids
I M Rybakowska, B Kutryb-Zając, R Milczarek, B Łukasz, E M Slominska, R T Smolenski
Nucleotide metabolism plays a major role in a number of vital cellular processes such as energetics. This, in turn, is important in pathologies such as atherosclerosis. Three month old atherosclerotic mice with knock outs for LDLR and apolipoprotein E (ApoE) were used for the experiments. Activities of AMP-deaminase (AMPD), ecto5'-nucleotidase (e5NT), adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP) were measured in heart, liver and kidney cortex and medulla by analysing conversion of substrates into products using HPLC...
May 21, 2018: Nucleosides, Nucleotides & Nucleic Acids
F Takayanagi, T Fukuuchi, N Yamaoka, K Kaneko
In this study, we investigated the alterations in the purine composition of swordfish prepared using a traditional Japanese processing method of soaking in sake lees. These alterations are the byproducts of the yeast fermentation of rice-koji and are renowned for enhancing the umami nature of food. Using a conventional assay method for hydrolyzing all of the purines into four bases and our developed method for simultaneously analyzing purines, we observed the alterations in four purine bases in the soaked sake lees and swordfish...
May 11, 2018: Nucleosides, Nucleotides & Nucleic Acids
Cesar Gonzalez, Maria de Cabrera, Stanislaw F Wnuk
Gemcitabine analogues with a lipophilic 4-N-alkyl chain bearing a terminal β-keto sulfonate moiety suitable for fluorination compatible with 18 F-radiolabeling have been explored. Displacement of p-toluenesulfonylamino in protected 4-N-tosylgemcitabine with 1-amino-10-undecene gave 4-N-(10-undecenyl)-3',5'-di-O-benzoyl-2'-deoxy-2',2'-difluorocytidine. Oxidation of the terminal double bond in the latter with OsO4 /NMO afforded 4-N-(10,11-dihydroxyundecanyl) derivative. Regioselective sulfonation of primary hydroxyl followed by oxidation of secondary hydroxyl with Collin's reagent yielded desired β-keto sulfonate analogues 8 or 9...
May 11, 2018: Nucleosides, Nucleotides & Nucleic Acids
Godefridus J Peters
The pyrimidine de novo nucleotide synthesis consists of 6 sequential steps. Various inhibitors against these enzymes have been developed and evaluated in the clinic for their potential anticancer activity: acivicin inhibits carbamoyl-phosphate-synthase-II, N-(phosphonacetyl)-L- aspartate (PALA) inhibits aspartate-transcarbamylase, Brequinar sodium and dichloroallyl-lawsone (DCL) inhibit dihydroorotate-dehydrogenase, and pyrazofurin (PF) inhibits orotate-phosphoribosyltransferase. We compared their growth inhibition against 3 cell lines from head-and-neck-cancer (HEP-2, UMSCC-14B and UMSCC-14C) and related the sensitivity to their effects on nucleotide pools...
May 3, 2018: Nucleosides, Nucleotides & Nucleic Acids
Srishylam Penjarla, S Rajendra Prasad, Dhande Sudhakar Reddy, Shyamapada Banerjee, Santhosh Penta, Yogesh S Sanghvi
Regioselective protection of primary hydroxyl group in nucleoside and carbohydrate analogs was accomplished using dimethoxytrityl alcohol (DMTr-OH) or dimethylpixyl alcohol (DMPx-OH) in presence of copper(II)nitrate as a Lewis acid catalyst. Excellent selectivity was observed for the protection of primary hydroxyl group over secondary while glycosidic bond remain unaffected. Utility of this methodology was further exemplified via DMTr- and DMPx-protection of alipahtic acyclic and cyclic diols.
May 3, 2018: Nucleosides, Nucleotides & Nucleic Acids
Galal H Elgemeie, Dina H El-Naggar
A novel method for preparation of a new class of dihydropyridine thioglycosides and their corresponding dehydrogenated forms, via reaction of piperidinium salts of dihydropyridinethiones with 2,3,4,6-tetra-O-acetyl-α-D-gluco- and galactopyranosyl bromides has been studied. The evaluation of antiproliferative activity against HepG-2 cell lines (liver carcinoma cell lines) of the dihydropyridine thioglycosides and pyridine thioglycosides revealed that many of the thioglycosides have interesting antitumor activities specifically 5c, 5g, 5l, 5o, 5p, 7a, 7i, 7p, 8b, 8f, 8s, and 8v...
May 3, 2018: Nucleosides, Nucleotides & Nucleic Acids
I Sebesta, B Stiburkova, J Krijt
Hereditary xanthinuria (type I) is caused by an inherited deficiency of the xanthine oxidorectase (XDH/XO), and is characterized by very low concentration of uric acid in blood and urine and high concentration of urinary xanthine, leading to urolithiasis. Type II results from a combined deficiency of XDH/XO and aldehyde oxidase. Patients present with hematuria, renal colic, urolithiasis or even acute renal failure. Clinical symptoms are the same for both types. In a third type, clinically distinct, sulfite oxidase activity is missing as well as XDH/XO and aldehyde oxidase...
May 3, 2018: Nucleosides, Nucleotides & Nucleic Acids
Berrie Meijer, Margien L Seinen, Tessa Hosman, Ronald K Linskens, Jan-Kees Kneppelhout, Godefridus J Peters, Chris Jj Mulder, Adriaan A van Bodegraven, Nanne Kh de Boer
OBJECTIVES: Thiopurines play an essential role in the management of inflammatory bowel diseases (IBD, i.e. Crohn's disease and ulcerative colitis). Over the past decade, several strategies to optimize treatment with thiopurines have been evaluated, including co-administration of allopurinol, a xanthine-oxidoreductase (XO) inhibitor, to low-dose thiopurine therapy. We aimed to assess the inter-individual variability of XO-activity between IBD-patients. METHODS: We assessed XO activity in serum of IBD-patients of two medical centers in The Netherlands using the Amplex® Red Xanthine/Xanthine Oxidase Assay Kit, which measures the superoxide formation in a coupled reaction to the red-fluorescent oxidation product, resofurine...
May 3, 2018: Nucleosides, Nucleotides & Nucleic Acids
Neha Rana, Manish Kumar, Ankita Singh, Jyotirmoy Maity, Poonam Shukla, Ashok K Prasad
Syntheses of novel 3'-azido-3'-deoxy-2'-O,4'-C-methylene-α-L-ribofuranosyl nucleosides have been carried out from 3'-azido-3'-deoxy-4'-C-hydroxymethyl-β-D-xylofuranosyl nucleosides following both chemical and chemo-enzymatic methodologies. The precursor nucleoside in turn was synthesized from a common glycosyl donor 4-C-acetoxymethyl-1,2,5-tri-O-acetyl-3-azido-3-deoxy-α,β-D-xylofuranose, which was obtained by the acetolysis of 4-C-acetoxymethyl-5-O-acetyl-3-azido-3-deoxy-1,2-O-isopropylidene-α-D-xylofuranose in 96% yield...
May 3, 2018: Nucleosides, Nucleotides & Nucleic Acids
N Yamada, C Saito, Y Murayama-Chiba, H Kano, Y Asami, H Itoh
Excessive intake of purine-rich foods elevates serum uric acid levels, making it a risk factor for hyperuricemia. We hypothesized that lactic acid bacteria ingested with food might utilize purines and contribute to their decreased absorption in the intestines, thereby preventing hyperuricemia. We previously reported that Lactobacillus gasseri PA-3 (PA-3) incorporates adenosine/inosine and related purines and that oral ingestion of PA-3 reduced the absorption of these purines in rats. However, it is unclear whether PA-3 also decreases the absorption of other purines, such as guanosine 5'-monophosphate (GMP) and guanosine...
May 3, 2018: Nucleosides, Nucleotides & Nucleic Acids
M Löffler, E A Carrey, E Zameitat
Since 1956, when exogenous uridine and cytidine were found to be necessary for the maintenance of perfused rat brain function, the co-existence of de novo synthesis, salvage pathways and removal of pyrimidine bases in the CNS has been a controversial subject. Here, we review studies on metabolites and enzymes of pyrimidine metabolism through more than 60 years. In view of known and newly-described inherited pyrimidine and purine disorders - some with complex clinical profiles of neurological impairments - we underline the necessity to investigate how the different pathways work together in the developing brain and then sustain plasticity, regeneration and neuro-transmission in the adult CNS...
April 25, 2018: Nucleosides, Nucleotides & Nucleic Acids
T Fukuuchi, N Iyama, N Yamaoka, K Kaneko
Ribonucleotide flavor enhancers such as inosine monophosphate (IMP) and guanosine monophosphate (GMP) provide umami taste, similarly to glutamine. Japanese cuisine frequently uses soup stocks containing these nucleotides to enhance umami. We quantified 18 types of purines (nucleotides, nucleosides, and purine bases) in three soup stocks (chicken, consommé, and dried bonito soup). IMP was the most abundant purine in all umami soup stocks, followed by hypoxanthine, inosine, and GMP. The IMP content of dried bonito soup was the highest of the three soup stocks...
April 13, 2018: Nucleosides, Nucleotides & Nucleic Acids
Rosa J Torres, Juan G Puig
The neurological manifestations of Lesch-Nyhan disease (LND) have been attributed to the effect of hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency on nervous system development. An increase has been reported in the levels of 5-aminoimidazole-4-carboxamide-1-β-D-ribotide (AICAR) and its triphosphate form ZTP in the red blood cells of patients with LND. AICAR accumulation in the brain has been hypothesized as the cause of some of the neurological symptoms of patients with LND. In this study, we examined the effect of AICAR on the differentiation of neurons in the well-established human NTERA-2 cl...
April 10, 2018: Nucleosides, Nucleotides & Nucleic Acids
Katarzyna Lubecka, Agnieszka Kaufman-Szymczyk, Krystyna Fabianowska-Majewska
Many antineoplastic nucleoside analogue-based combinatorial strategies focused on remodelling aberrant DNA methylation patterns have been developed. The number of studies demonstrate high efficacy of bioactive phytochemicals in support of conventional chemotherapy. Our recent discoveries of the epigenetic effects of clofarabine (2'-deoxyadenosine analogue, antileukaemic drug) and clofarabine-based combinations with dietary bioactive compounds in breast cancer cells led us to look for more DNA methylation targets of these cancer-preventive agents...
April 10, 2018: Nucleosides, Nucleotides & Nucleic Acids
Jeremy E B McCallum, Christopher W Coyle, Ryan R Elson, Blake A Titterington
The development of small molecules to stabilize the G-quadruplex structure has garnered significant attention for anticancer drug discovery. Herein, we report the synthesis of several 4,4'-diaminoazobenzene derivatives containing different substituent groups and their ability to bind and stabilize telomeric G-quadruplex DNA. Circular dichroism (CD) spectroscopy was performed to characterize the quadruplex topologies, measure stabilization effects, and evaluate their capabilities for conformational photoregulation...
March 12, 2018: Nucleosides, Nucleotides & Nucleic Acids
Galal H Elgemeie, Nahed M Fathy, Ayman B Farag, Sheikha A Alkhursani
A novel series of acyclic pyridine thioglycosides has been synthesized. Evaluation of the anti proliferative activity of these compounds against HEPG-2 cell lines (liver carcinoma cell lines) shows that most of the compounds have high anti-tumor activities especially 6b, 6c, 7b and 7c. Furthermore, in the modeling study, these compounds showed that they have high binding affinity with thymidylate synthase dihydrofolate reductase (TS-DHFR).
March 4, 2018: Nucleosides, Nucleotides & Nucleic Acids
Fida Muhammad Khan, Kainaat William, Samreen Aruge, Safia Janjua, Safdar Ali Shah
Illegal trade is a major threat to the biodiversity and the efforts initiated for the conservation of wildlife. The shortcomings of the traditional taxonomic identification methods have been coped by a revolutionary and emerging technique, the "DNA (Deoxyribonucleic Acid) barcoding". Here we report a case of trader who was allegedly making footwear for a famous international celebrity from wild animal cutis. The samples confiscated during a raid on a footwear manufacturing industry by KP Wildlife department in August, 2016, were received by Bioresource Research Centre (BRC) for molecular identification on 1st September, 2016...
March 4, 2018: Nucleosides, Nucleotides & Nucleic Acids
Nahid Shahabadi, Farshad Shiri, Saba Hadidi
The interaction between the dimer structure of ibuprofen drug (D-IB) and calf thymus DNA under simulative physiological conditions was investigated with the use of Hoechst 33258 and methylene blue dye as spectral probes by the methods of UV-visible absorption, fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling study.Using the Job's plot, a single class of binding sites for theD-IB on DNA was put in evidence. The Stern-Volmer analysis of fluorescence quenching data shows the presence of both the static and dynamic quenching mechanisms...
March 4, 2018: Nucleosides, Nucleotides & Nucleic Acids
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