Synthesis and structure of novel conformationally constrained 1',2'-azetidine-fused bicyclic pyrimidine nucleosides: their incorporation into oligo-DNAs and thermal stability of the heteroduplexes

[structures: see text] The synthesis of novel 1',2'-aminomethylene bridged (6-aza-2-oxabicyclo[3.2.0]heptane) "azetidine" pyrimidine nucleosides and their transformations to the corresponding phosphoramidite building blocks (20, 39, and 42) for automated solid-phase oligonucleotide synthesis is reported. The novel bicyclonucleoside "azetidine" monomers were synthesized by two different strategies starting from the known sugar intermediate 6-O-benzyl-1,2:3,4-bis-O-isopropylidene-D-psicofuranose. Conformational analysis performed by molecular modeling (ab initio and MD simulations) and NMR showed that the azetidine-fused furanose sugar is locked in a North-East conformation with pseudorotational phase angle (P) in the range of 44.5-53.8 degrees and sugar puckering amplitude (phi(m)) of 29.3-32.6 degrees for the azetidine-modified T, U, C, and 5-Me-C nucleosides. Thermal denaturation studies of azetidine-modified oligo-DNA/RNA heteroduplexes show that the azetidine-fused nucleosides display improved binding affinities when compared to that of previously synthesized North-East sugar constrained oxetane fused analogues.     

Regioselective syntheses of 7-nitro-7-deazapurine nucleosides and nucleotides for efficient PCR incorporation

Substitution at the C(7) position of purine nucleotides by a potent electron-withdrawing nitro group facilitates the cleavage of glycosidic bonds under alkaline conditions. This property is useful for sequence-specific cleavage of DNA containing these analogues. Here we describe the preparation of 7-deaza-7-NO(2)-dA and 7-deaza-7-NO(2)-dG using two different approaches, starting from 2'-deoxy-adenosine and 6-chloro-7-deaza-guanine, respectively. These modified nucleosides were converted to nucleotide triphosphates, each of which can replace the corresponding, naturally occurring triphosphate to support PCR amplification. [structure: see text]     

Analogs of pyrimidine nucleosides

The UV absorption spectra of 5-substituted N¹-(tetrahydrofuran-2-yl)- and N¹-(2oxotetrahydrofuran-3-yl)uracils have been studied and their protolysis constants have been determined by the spectrophotometric method. A comparison is given with the spectra and pKa values of the corresponding N¹-methyl derivatives and ribosides and deoxyribosides.For part IV see [11].The work was carried out with analytical samples of compounds obtained by us previously [9–12].     

Synthesis of N3-substituted uridine and related pyrimidine nucleosides and their antinociceptive effects in mice

Seventy eight N(3)-substituted derivatives of uridine (1), thymidine (2), 2'-deoxyuridine (3), 6-azauridine (4), 2',3'-O-isopropylideneuridine (5), and arabinofuranosyluracil (6) were synthesized and their antinociceptive effects were evaluated. N(3)-(2',4'-Dimethoxyphenacyl)uridine (1l), N(3)-(2',4'-dimethoxyphenacyl)2'-deoxyuridine (3l), and N(3)-(2',5'-dimethoxyphenacyl)arabinofuranosyluracil (6m) possessed 93, 86, and 82% of the antinociceptive effects tested by hot plate, respectively. The antinociceptive effects of three derivatives were 5.8, 5.4, and 5.1-folds of the effect of N(3)-phenacyluridine (1h) (16%), respectively. The structure-activity relationship of N(3)-substituted pyrimidine nucleosides was also discussed.     

Analogs of pyrimidine nucleosides

N₁-(-Tetrahydrofuranyl)- and N₁-(-tetrahydropyranyl)uracils and the corresponding 6-azauracils have been obtained by the condensation of bistrimethylsilyl derivatives of uracils and 6-azauracils with-chlorotetrahydrofuran and-chlorotetrahydropyran. The superiority of the silyl method over the mercury method used previously has been demonstrated.For part III, see [9].     

Analogs of pyrimidine nucleosides

α-(1-Cytosinyl)-γ-butyrolactone was obtained by condensation of bis(trimethylsilyl)cytosine with α-bromobutyrolactone. The reduction of α-(1-cytosinyl)-γ-butyrolactone with sodium borohydride gave N₁-(1,4-dihydroxy-2-butyl)cytosine, the acylation of which with benzoyl chloride and subsequent partial hydrolysis gave N₁-(1,4-dihydroxy-2-butyl)-N₄-benzoylcytosine.     

Analogs of pyrimidine nucleosides

The reaction of alkoxy bromides with N₁-(-tetrahydrofuryl) derivatives of pyrimidine bases has given a series of 6-alkoxy-5-bromo-1-(-tetrahydrofuryl)-5, 6-dihydrouracils. The hydrogenation of the 1-(-tetrahydrofuryl) derivatives of uracil and of 5-fluorouracil has been studied. It has been shown that in both cases 1-(-tetrahydrofuryl)-5, 6-dihydrouracil is formed.     

Analogs of pyrimidine nucleosides

A number of N₁-(-butyrolactono) derivatives of 5-substituted uracils have been synthesized by condensing the sodium derivatives of the corresponding bases with -bromobutyrolactone or by the halogenation of N₁-(-butyrolactono)uracil.For part I, see [1].     

Analogs of pyrimidine nucleosides

A new method was developed for the synthesis of 1-(2-tetrahydrofuryl) derivatives of uracil, 5-substituted uracils, 6-azauracil, and cytosine by alkylation of 2,4-bis(trimethylsilyl) derivatives of pyrimidine bases with 2-acetoxytetrahydrofuran in the presence of Lewis acids. In contrast to 2-chlorotetrahydrofuran, which is used in a previously described method, 2-acetoxytetrahydrofuran is stable at room temperature and reacts under these conditions with silyl derivatives of uracils in the presence of SnCl₄ to give 1-(2-tetrahydrofuryl) derivatives of pyrimidine bases in 80–85% yields.See [1] for communication X.Deceased.Translated from Khimiya Geterotsiklicheskikh Soedineaii, No. 9, pp. 1258–1259. September, 1977.     

Analogs of pyrimidine nucleosides

A new method for the synthesis ofN₁-(dihydroxyalkyl)uracils by reduction of substituted α- (1-uracilyl)- and γ-[(1-uracilyl)methyl]-γ-butyrolactones with sodium borohydride was found.     

Analogs of pyrimidine nucleosides. 16. Racemic 2′,3′-dideoxynucleosides and their derivatives

The chlorination of 2-halomethyltetrahydrofurans and acyl derivatives of tetrahydrofuryl alcohol wasstudied; mixtures of 2,5- and 2,2-disubstituted tetrahydrofurans are formed as a result of the reaction. 2,4-Bis(trimethylsilyl) derivatives of uracil, 5-substituted uracils, and cytosine are alkylated by the resulting mixtures of -chloro ethers without separation, and mixtures of cis and transisomers of 1-(5-substituted-2-tetrahydrofuryl) and 1-(2-substituted-2-tetrahydrofuryl) derivatives of uracil, 5-substituted uracils, and cytosine are obtained. The reaction products were identified onthe basis of their PMR spectra.See [1] for Communication 15.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 101–110, January, 1982.     

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.     

Interaction of low-energy electrons with the pyrimidine bases and nucleosides of DNA

We report computed cross sections for the elastic scattering of slow electrons by the pyrimidine bases of DNA, thymine and cytosine, and by the associated nucleosides, deoxythymidine and deoxycytidine. For the isolated bases, we carried out calculations both with and without the inclusion of polarization effects. For the nucleosides, we neglect polarization effects but estimate their influence on resonance positions by comparison with the results for the corresponding bases. Where possible, we compare our results with experiment and previous calculations.     

DNA molecules site-specific immobilization and their applications

In addition to its role as a carrier of genetic information, DNA has been recognized as a construction material for the assembly of different objects and structural arrangements with nanoscale features. As a result of DNA’s self-recognition properties (based on the specific base-pairing of G-C and T-A), monolayer films of nucleic acids on solid supports have attracted an escalating attentions. Recently, numerous novel materials based on two-dimensional (2D) and three-dimensional (3D) DNA structures have been reported, which extends their utility to a large number of appliations. This review paper intends to be a new and comprehensive overview of recent strategies to site-specifically immobilized DNA on various materials, including carbonaceous substances, gold, and silica substrate, emphasizing the applications of site-specific DNA nanostructure-based devices for diagnostic, bioanalytical, food safety and environmental monitoring. Additionally, an up-to-date perspective is proposed at the end of this review.      

Stereospecific incorporation of 13CO into olefinic substituted metal carbonyl compounds

The triene complex, (bicyclo[6.1.0] nona-2,4,6-triene)molybdenum tricarbonyl, has been observed to react with ¹³CO in solution to afford stereospecifically the axially labelled ¹³CO tetracarbonyl derivative. Further reactions of this ¹³CO derivative with triphenylphosphine or bis(1,2-diphenylphosphino)ethane resulted in formation of the cis disubstituted phosphine derivatives with retention of the ¹³CO label.     

Stereospecific syntheses of 4-methylnaphthoquinol epoxide

Epoxidation of 4-methylnaphthoquinol (1) with alkaline hydrogen peroxide and addition of methyllithium to naphthoquinõne epoxide both lead stereospecifically to the $\text{cis}$ hydroxyepoxide (2).     

Analogs of the pyrimidine nucleosides

The kinetics of the hydrolysis of the pseudoglycosidic C-N bond in the N¹-derivatives of uracil, thymine, and 5-fluorouracil at various pH values of the medium have been studied. The dependence of the rate of hydrolysis of N¹-(tetrahydrofuran 2-yl)-5-fluorouracil on the temperature has been investigated. The influence of substituants at C₅ and N₁ of the pyrimidine ring on the stability of the pseudoglycosidic C-N bond has been evaluated.For part V, see [10].     

Retraction: Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases

Retraction of ‘Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases’ by Ai Tran et al., Chem. Sci., 2020, 11, 11818–11826, DOI: 10.1039/D0SC04161K.

The Royal Society of Chemistry hereby wholly retracts this Chemical Science article due to concerns about the reproducibility of the data.The Royal Society of Chemistry has been contacted by the authors of this article to alert us that recent experiments by their group have shown that some results are not reproducible, especially the yields of several key intermediates. Given the focus on the easy access to epigenetically important nucleosides and related ODNs, unreliable yields significantly impact the confidence in the results. In addition, it was discovered that one of the biological samples provided to the authors was mislabelled. The human stem cells were actually mouse stem cells, hence some discussion and conclusions in the article may no longer apply. Ahead of a thorough re-examination of the entire study, in order to preserve the rigor of the scientific record, the signing authors have chosen to retract the article and they would like to apologise for any inconvenience this may have caused for readers.Signed: Ai Tran, Song Zheng, Dawanna S. White, Alyson M. Curry and Yana CenRetraction endorsed by May Copsey, Executive Editor, Chemical Science     

Ultrasound-assisted green syntheses of novel pyrimidine derivatives and their comparison with conventional methods

Ultrasound-assisted green syntheses of novel potentially bioactive pyrimidine derivatives have been carried out. The same compounds were obtained by conventional methods of synthesis, and the reaction times and yields of final products obtained by these two methods were compared. It was found that the time of utrasound-promoted reactions was reduced by almost 6–96 times, and their yields were equal or turn out to be greater compared to the traditional approach. The synthesized compounds showed a pronounced stimulating effect on plant growth. The most active derivatives were selected for deeper biological studies and subsequent field trials.