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...     

Enzymatic Synthesis of Fructosyl Glycerol

ABSTRACT

The enzymatic synthesis of ß2-2' and ß2-1'-D- fructopyranosyl glycerol was carried out with levansucrase from Bacillus circulans or B.subtilis, using sucrose as fructosyl donor and glycerol. The specificity and efficiency of the enzyme was modified by controlling both the water and the total substrate concentrations. The products were purified by HPLC and analyzed by ¹H, ¹³C NMR and GC-MS.     

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.     

Synthesis of Disaccharide Nucleosides by the O‐Glycosylation of Natural Nucleosides with Thioglycoside Donors

Disaccharide nucleosides constitute an important group of naturally‐occurring sugar derivatives. In this study, we report on the synthesis of disaccharide nucleosides by the direct O‐glycosylation of nucleoside acceptors, such as adenosine, guanosine, thymidine, and cytidine, with glycosyl donors. Among the glycosyl donors tested, thioglycosides were found to give the corresponding disaccharide nucleosides in moderate to high chemical yields with the above nucleoside acceptors using p‐toluenesulfenyl chloride (TolSCl) and silver triflate (AgOTf) as promoters. The interaction of these promoters with nucleoside acceptors was examined by ¹H NMR spectroscopic experiments.     

Copper/Graphene/Clay Nanohybrid: A Highly Efficient Heterogeneous Nanocatalyst for the Synthesis of Novel 1,2,3‐Triazolyl Carboacyclic Nucleosides via ‘Click’ Huisgen 1,3‐Dipolar Cycloaddition

A very mild and highly efficient synthesis of some novel 1H‐1,2,3‐triazolyl carboacyclic nucleosides via a ‘Click’ Huisgen cycloaddition of N‐propargyl nucleobases and azido alcohols using Cu/aminoclay/reduced graphene oxide nanohybrid (Cu/AC/r‐GO nanohybrid) as nanocatalyst is described. The preparation and characterization of Cu/AC/r‐GO nanohybrid are discussed. This catalyst was characterized by X‐ray diffraction, FT‐IR, TEM, and energy‐dispersive analysis of X‐ray techniques. Cu/AC/r‐GO nanohybrid is a stable and highly efficient heterogeneous nanocatalyst that can be easily prepared, used, and restored from the reaction mixture by simple filtration, and reused for many consecutive trials without significant decrease in activity.     

Isoguanine and 5‐Methyl‐Isocytosine Bases,In Vitro and In Vivo

The synthesis, base‐pairing properties and in vitro and in vivo characteristics of 5‐methyl‐isocytosine (isoC^Me) and isoguanine (isoG) nucleosides, incorporated in an HNA(h) (hexitol nucleic acid)–DNA(d) mosaic backbone, are described. The required h‐isoG phosphoramidite was prepared by a selective deamination as a key step. As demonstrated by T_m measurements the hexitol sugar showed slightly better mismatch discrimination against dT. The d‐isoG base mispairing follows the order T>G>C while the h‐isoG base mispairing follows the order G>C>T. The h‐ and d‐isoC^Me bases mainly mispair with G. Enzymatic incorporation experiments show that the hexitol backbone has a variable effect on selectivity. In the enzymatic assays, isoG misincorporates mainly with T, and isoC^Me misincorporates mainly with A. Further analysis in vivo confirmed the patterns of base‐pair interpretation for the deoxyribose and hexitol isoC^Me/isoG bases in a cellular context, through incorporation of the bases into plasmidic DNA. Results in vivo demonstrated that mispairing and misincorporation was dependent on the backbone scaffold of the base, which indicates rational advances towards orthogonality.     

Pyrrolo‐dC Metal‐Mediated Base Pairs in the Reverse Watson–Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6‐Pyridinyl Residues on Fluorescence and Silver‐Ion Binding

Reverse Watson–Crick DNA with parallel‐strand orientation (ps DNA) has been constructed. Pyrrolo‐dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3‐d]pyrimidine base have been incorporated in 12‐ and 25‐mer oligonucleotide duplexes and utilized as silver‐ion binding sites. Thermal‐stability studies on the parallel DNA strands demonstrated extremely strong silver‐ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single ^2pyPyrdC–^2pyPyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver‐ion base pair that aligns 7‐deazapurine bases head‐to‐tail instead of head‐to‐head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson–Crick base pairs stabilized by a dinuclear silver‐mediated PyrdC pair.     

Cycloaddition Reactions of Deoxyribosylpropynoates

Pure anomers of either α or β 3-(2-deoxyribofuranosyl)propynoates reacted with the tetramethylcyclobutadiene–aluminum trichloride complex to yield the corresponding diastereoisomeric Dewar benzenes. Thermal- or ultraviolet light–initiated rearrangement gave rise to highly substituted C-aryldeoxyribosides as single anomers. The same compounds as well as other substituted deoxyribosides were obtained also by transition metal–mediated cycloaddition reactions.     

Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks--on the benefit of restoring the cyclic sugar backbone

Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.