Synthesis of oligo-2′-<Emphasis Type="Italic">O</Emphasis>-methylribonucleotides containing α-amino acid residues in 2′-position

Oligo-2′-O-methylribonucleotides containing residues of phenylalanine, histidine, and lysine amides were synthesized with the use of new phosphoramidites of 2′-aminoacid derivatives of uridine. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 775–783, April, 2007.     

A new method for inversion of hydroxyl group of carbocyclic nucleosides

The hydroxyl group of carbocyclic nucleosides was inversed when the compounds were treated with Me_3SiCl,KCN and a catalytic amount of NaI in DMF/CH_3CN.     

5′-Noraristeromycin derivatives isomeric to aristeromycin and 2′-deoxyaristeromycin

A straightforward synthesis of (1S,2R,3R,4R)-4-(6-aminopurin-9-yl)-2-hydroxymethylcyclopentane-1,3-diol (2), an isomer of aristeromycin, and its 2′-deoxy derivative 3 from readily available disubstituted cyclopentenes is presented. An antiviral analysis of 2 showed it to have significant activity versus Epstein-Barr virus (IC₅₀ 0.62 μg/mL in the Elisa assay) and to be free of cytotoxicity effects against the host cells. In a much less comprehensive antiviral analysis, 3 also was active towards Epstein-Barr (IC₅₀ 7.58 μg/mL in the Elisa assay) but this was accompanied by cellular toxicity.     

Advantages of the Ns group in the reactions of N-SO2R inosines with benzylamine and with NH3

The reactivity of N¹-alkylsulfonyl- and N¹-arylsulfonyl-2′,3′,5′-tri-O-acetylinosine with benzylamine and with ¹⁵NH₃, regarding the attack on C2, has been shown to be in the order CF₃SO₂ (Tf) > 2,4-(NO₂)₂C₆H₃SO₂ (DNs) ? 4-NO₂C₆H₄SO₂ (pNs) ≈ C₆F₅SO₂ (PFBs) > 2-NO₂C₆H₄SO₂ (Ns) ? CH₃SO₂ (Ms) > 4-CH₃C₆H₄SO₂ (Ts) > 2,4,6-(CH₃)₃C₆H₂SO₂ (Mts). In spite of its intermediate reactivity, the Ns group is the most appropriate, since in this case the formation of by-products is minimised during the ring-opening and ring-closing steps of the process. Another advantage of the Ns group is thus disclosed.     

Interaction of bis-aryl functionalized molecules with nucleosides and nucleic acids

A series of novel molecules with a cyclen(1,4,7,10-tetraazacyclododecane) moiety appended on and bearing different aromatic fragments in the structures were synthesized and characterized.The binding activities of these compounds towards DNA were systematically studied by spectroscopic,viscometric and gel electrophoresis methods.The results suggest that the stacking interaction plays an important role in improving the DNA binding ability of the compounds.The binding modes of the compounds towards DNA are als...     

Ultrasensitive Simultaneous Detection of Multiple Rare Modified Nucleosides as Promising Biomarkers in Low-Put Breast Cancer DNA Samples for Clinical Multi-Dimensional Diagnosis

Early cancer diagnosis is essential for successful treatment and prognosis, and modified nucleosides have attracted widespread attention as a promising group of cancer biomarkers. However, analyzing these modified nucleosides with an extremely low abundance is a great challenge, especially analyzing multiple modified nucleosides with a different abundance simultaneously. In this work, an ultrasensitive quantification method based on chemical labeling, coupled with LC-MS/MS analysis, was established for the simultaneous quantification of 5hmdC, 5fdC, 5hmdU and 5fdU. Additionally, the contents of 5mdC and canonical nucleosides could be obtained at the same time. Upon derivatization, the detection sensitivities of 5hmdC, 5fdC, 5hmdU and 5fdU were dramatically enhanced by several hundred times. The established method was further applied to the simultaneous detection of nine nucleosides with different abundances in about 2 μg genomic DNA of breast tissues from 20 breast cancer patients. The DNA consumption was less than other overall reported quantification methods, thereby providing an opportunity to monitor rare, modified nucleosides in precious samples and biology processes that could not be investigated before. The contents of 5hmdC, 5hmdU and 5fdU in tumor tissues and normal tissues adjacent to the tumor were significantly changed, indicating that these three modified nucleosides may play certain roles in the formation and development of tumors and be potential cancer biomarkers. While the detection rates of 5hmdC, 5hmdU and 5fdU alone as a biomarker for breast cancer samples were 95%, 75% and 85%, respectively, by detecting these three cancer biomarkers simultaneously, two of the three were 100% consistent with the overall trend. Therefore, simultaneous detection of multiple cancer biomarkers in clinical samples greatly improved the accuracy of cancer diagnosis, indicating that our method has great application potential in clinical multidimensional diagnosis.     

Applications of synthetic oligoribonucleotide analogues in studies of RNA structure and function

The study of RNA structure and function has been considerably aided by the development of methods for the chemical synthesis of oligoribonucleotides into which have been incorporated modified nucleosides carrying site-specific alterations. Such modifications are designed to eliminate or alter individual functional groups in the RNA which potentially can take part in hydrogen-bonding or other non-covalent interactions. Comparison of the properties of the modified RNA with unmodified RNA models allows conclusions to be drawn concerning the importance or otherwise of specific functional groups within the RNA. The methods have been applied to studies of RNA structure, RNA catalysis, and interactions of RNA with proteins.