Template atom transfer radical polymerization of a diaminopyrimidine‐derivatized monomer in the presence of a uracil‐containing polymer

Uracil‐derivatized monomer 6‐undecyl‐1‐(4‐vinylbenzyl)uracil and diaminopyrimidine‐derivatized monomer 2,6‐dioctanoylamido‐4‐methacryloyloxypyrimidine (DMP) were synthesized and polymerized by atom transfer radical polymerization (ATRP). A well‐defined, highly soluble, uracil‐containing polymer, poly[6‐undecyl‐1‐(4‐vinylbenzyl)uracil] (PUVU), was prepared in dioxane at 90 °C with CuBr/1,1,4,7,10,10‐hexamethyltriethylenetetramine as the catalyst and methyl α‐bromophenylacetate as the initiator. PUVU was further used as a template for the ATRP of DMP. The enhanced apparent rate constant of the DMP polymerization in the presence of PUVU indicated that the ATRP of DMP occurred along the PUVU template. The template polymerization produced a stable and insoluble macromolecular complex, PUVU/poly(2,6‐dioctanoylamido‐4‐methacryloyloxypyrimidine). An X‐ray diffraction study confirmed that the complex had strandlike domains. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6607–6615, 2006     

Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs

Molecular dynamics simulations of double-helical DNA oligomers have been performed to investigate differences in the structure, dynamics, and hydration of F-F and T-T mispairs. Hexamers containing F-F pairs were found to be more dynamic, especially in the region of the mispair itself. This dynamic variability derives from greater flexibility of F-F pairs. The T-T mispairs, on the other hand, were found to be comparatively tightly bound as wobble pairs. The major and minor groove edges of the T-T pairs were observed to be solvated at exposed carbonyl positions by at least one water molecule, while F-F pairs lacked solvating waters. Stacking interactions were nearly identical for T-T and F-F pairs, leading to similar average structures, even though F stacking was more dynamically variable. Solvation differences between F-F and T-T therefore support the steric exclusion model for nucleotide incorporation in DNA replication. Large differences in the orientation of minor groove functional groups, in addition to differences in solvation, further rationalize why F bases present during DNA extension events induce stalls. Two novel nucleotides are proposed to further elucidate minor groove interactions of DNA with polymerase molecules.Electronic Supplementary Material This Material consists of equilibration protocol, plots of center-of-mass stacking, water radial distribution functions, helical parameter dynamics, and dynamics data for a control AT sequence. Supplementary material is available in the online version of this article at Contribution to the Jacopo Tomasi Honorary Issue     

Synthesis of a Photolabeling Probe for the Study of Antiviral Mechanism of Ribavirin

Ribavirin has been used in urgency to treat SARS patients recently. In order to study its antiviral mechanism by photolabeling approach, we have synthesized and characterized 5-azido-1-β-D-ribofuranosyl-1,2,4-triazole-3-carboxiamide 1 as a photolabeling probe of ribavirin. The azidotriazole nucleoside showed rapid and clean photochemical reaction, suggesting that 1 is a promising probe to study the antiviral mechanism ofribarivin by photolabeling.     

A simple and simultaneous determination of acyclovir and ganciclovir in human plasma by high-performance liquid chromatography

A simple high-performance liquid chromatographic method was developed for the simultaneous determination of the therapeutic levels of acyclovir and ganciclovir in human plasma. After precipitation of plasma proteins with 6% perchloric acid, acyclovir and ganciclovir were simultaneously determined by reversed-phase chromatography with spectophotometric detection at 254 nm. The peak heights for acyclovir and ganciclovir were linearly related to their concentrations ranging from 0.063 to 2.080 micro g/mL. The recovery was 100.48-102.84% for acyclovir and 99.26-103.07% for ganciclovir. The intra- and inter-day relative standard deviation values were in the range 0.186-8.703% for acyclovir and 0.137-6.424% for ganciclovir. The detection limits for both compounds were 0.01 micro g/mL determined as the signal-to-noise ratio of 3. The present method is applicable to therapeutic monitoring during antiviral medication.     

An Efficient Synthesis of 8-Amino-9-Benzylguanine

The reaction of 2,5-diamino-4-benzylamino-pyrimidin-6(III)-one (6) with benzoyl isothiocyanate furnished 2-amino-4-benzylamino-5-[1-(3-benzoylthioureido)]-pyrimidin-6(1H)-one (7) in good yield. The title compound I was synthesized from compound 7 via a cyclodesulfurative reaction with DCC in DMF at 80°C directly to form 8-benzoylamino-9-benzylguanine (9) which was subsequently treated with 1 N sodium hydroxide.     

Pulse radiolysis of one-electron oxidation of rare tricyclic nucleoside derivative

~~Pulse radiolysis of one-electron oxidation of rare tricyclic nucleoside derivative@赵红卫$Shanghai Institute of Nuclear Research, Chinese Academy of Sciences! Shanghai 201800,China @江致勤$Department of Chemistry, Tongji Unviersity!Shanghai 200092,China @窦大营$Shanghai Institute of Nuclear Research, Chinese Academy of Sciences! Shanghai 201800,China @吴铁一$Shanghai Institute of Nuclear Research, Chinese Academy of Sciences! Shanghai 201800,China @王文锋$Shanghai…     

Synthesis of l,l-puromycin

l,l-Puromycin, a diastereomer of the natural peptidyl nucleoside antibiotic puromycin, has been synthesized from l-xylose in 13 steps.     

A New Alkylation-Elimination Method for Synthesis of Antiviral Fluoromethylenecyclopropane Analogues of Nucleosides

A new method for the synthesis of fluoromethylenecyclopropane nucleosides by alkylation-elimination procedure is described. Fluorination of methylenecyclopropane carboxylate 6 gave fluoroester 7. Treatment of 7 with phenylselenenyl bromide afforded the desired ethyl (E)-2-bromomethyl-1-fluoro-2-phenylselenenylcyclopropane-1-carboxylate 11 in 85% yield. DIBALH reduction of 11 gave 13, which after acetylation to 14 was reacted with 2-amino-6-chloropurine to give the 9-alkylated product 15 in 87% yield. Se-oxidation of 15 with hydrogen peroxide afforded 16, which underwent smooth elimination in a mixture of THF-DMF at 60 °C giving rise to a Z,E mixture of protected nucleosides 17. Deacetylation gave Z-1a and E-1a which were separated on a silica gel column. Both Z-1a and E-1a were converted into the respective guanine analogues Z-1b and E-1b.     

Interaction between peroxide ion and phenol group which are coordinated to the same iron(III) ion

We have prepared several new iron(III) complexes with ligands which contain a phenol group; these are tetradentate [(X-phpy)H, X and H(phpy) represent the substituents on the phenol ring and N,N-bis(2-pyridylmethyl)-N-(2-hydroxybenzyl)amine, respectively] and pentadentate ligands [(R-enph-X)H; R=ethyl(Et) or methyl(Me) derivative and H(Me-enph) denotes N,N-bis(2-pyridylmethyl)-N″-methyl-N″-(2″-hydroxyl-benzylamine)ethylenediamine] and have determined the crystal structures of Fe(phpy)Cl₂, Fe(5-NO₂-phpy)Cl₂, and Fe(Me-enph)ClPF₆, which are of a mononuclear six-coordinate iron(III) complex with coordination of one or two chloride ion(s). These compounds are highly colored (dark violet) due to the coordination of phenol group to an iron(III) atom. When hydrogen peroxide was added to the solution of the iron(III) complex, a color change occurs with bleaching of the violet color, indicating that oxidative degradation of the phenol moiety occurred in the ligand system. The bleaching of the violet color was also observed by the addition of t-butylhydroperoxide. The rate of the disappearance of the violet color is highly dependent on the substituent on the phenol ring; introduction of an electron-withdrawing group in the phenol ring decreases the rate of bleaching, suggesting that disappearance of the violet band should be due to a chemical reaction between the phenol group and a peroxide adduct of the iron(III) species with an η¹-coordination mode and that in this reaction the peroxide adduct acts as an electrophile towards phenol ring. The intramolecular interaction between the phenol moiety and an iron(III)-peroxide adduct may induce activation of the peroxide ion, and this was supported by several facts that the solution containing an iron(III) complex and hydrogen peroxide exhibits high activities for degradation of nucleosides and albumin.