Participation of the nucleobases in the regioselective backbone fragmentation of nucleic acids. A molecular dynamics and tandem mass spectrometric investigation on a model dinucleoside phosphotriester

The anions (I–III) obtained from O-methyl 5′-O-(5′-deoxythymidine) 3′-O-(2′,3′-dideoxyuridine) phosphate by the competitive removal of the 3-N-H protons of the nucleobases and of the methyl group from the phosphotriester bond, assume in the gas phase stable conformations as a function of their charge site. The mass-analyzed ion kinetic energy (MIKE) spectra of I and III show that the regioselective backbone cleavage of the internucleotidic linkage is controlled by the 2′-H proton transfer to the nucleobase within the 5′-end nucleoside. Similar pathways are taken by species II when the nucleobase is eliminated as neutral from the 5′-end nucleoside.     

Synthesis of Functionalized Diethyl(pyrrolidin-2-yl)phosphonate and Diethyl(5-oxopyrrolidin-2-yl)phosphonate

Short and efficient syntheses of functionalized (pyrrolidin-2-yl)phosphonate and (5-oxopyrrolidin-2-yl)phosphonate have been developed. The synthetic strategy involved the diastereospecific 1,3-dipolar cycloaddition of N-benzyl-C-(diethoxyphosphoryl)nitrone to cis-1,4-dihydroxybut-2-ene and dimethyl maleate, respectively. O,O-Diethyl 3-carbamoyl-4-hydroxy(5-oxopyrrolidin-2-yl)phosphonate was obtained from O,O-diethyl 2-benzyl-4,5-dimethoxycarbonyl(isoxazolidin-3-yl)phosphonate by hydrogenation and subsequent treatment with ammonia, whereas transformation of O,O-diethyl 2-benzyl-4,5-dihydroxymethyl(isoxazolidin-3-yl)phosphonate into O,O-diethyl 3-aminomethyl-4-hydroxy(pyrrolidin-2-yl)phosphonate was accomplished by mesylation followed by hydrogenolysis to undergo intramolecular cyclization and the introduction of amino group via ammonolysis. Stereochemistry of the isoxazolidine cycloadducts, as well as the final functionalized (pyrrolidin-2-yl)- and (5-oxopyrrolidin-2-yl)phosphonates were established based on conformational analyses using vicinal H–H, H–P, and C–P couplings and supported by the observed diagnostic NOESY correlation signals.     

Synthesis and herbicidal activities of methyl-1-(2,4-dichlorophenoxyacetoxy)alkylphosphonate monosalts

A series of 1-(2,4-dichlorophenoxyacetoxy)alkylphosphonic acid dimethyl esters 5 and its corresponding phosphonate monosalts 6 were synthesized as potential herbicide. The phosphonate monosalts can be prepared from 1-(2,4-dichlorophenoxyacetoxy)alkylphosphonic acid dimethyl esters 5, which were synthesized by the condensation of O,O-dimethyl-1-hydroxyalkylphosphonates with dichlorophenoxyacetic chloride. This method provides a simple and efficient procedure for the synthesis of phosphonate derivatives containing sensitive groups to acid, base or water such as carboxylate ester bond; and the herbicidal activity of title compounds was evaluated in a set of experiments in greenhouse. Most of the compounds exhibited notable herbicidal activity.     

Asymmetric organocatalytic conjugate addition of dialkyl phosphites to N-unprotected isatylidene malononitriles: access to 3-phospho-2-oxindoles with chiral quaternary stereocenters

The enantioselective Michael addition of dialkyl phosphites to N-unprotected isatylidene malononitriles has been established for the first time by using a simple bifunctional tertiary amine–thiourea catalyst. The corresponding adducts, 3-phospho-2-oxindoles, containing a chiral quaternary carbon center at the 3-position of the oxindole, were obtained in good to excellent yields (up to 98%) with moderate to excellent enantioselectivities (up to 95% ee). In addition, optically active 3,3′-disubstituted oxindoles bearing carboxylate and phosphonate groups were facilely obtained by the oxidative degradation of the Michael adducts.     

Selectively Deoxygenated Derivatives of β-Maltosyl-(1→4)-Trehalose as Biological Probes. II. the Synthesis of the 4- and 4′″-Monodeoxygenated Analogues

ABSTRACT

Two derivatives of β-maltosyl-(1→4)-trehalose monodeoxygenated at positions 4 or 4′″ have been synthesized in [2+2] block syntheses. After the preparation of precursors with only one free hydroxyl group the deoxy function was introduced by a Barton-McCombie reaction. Thus, glycosylation of 2,3,6-tri-O-benzyl-α-D-glucopyranosyl 2,3,6-tri-O-benzyl-α-D-glucopyranoside (4) with octa-O-acetyl-β-maltose (3) gave tetrasaccharide 5 with only one free hydroxyl group at the 4-position. The 4′-position of an allyl maltoside was available selectively after removal of a 4′,6′-cyclic acetal and selective benzoylation of the 6′-position. Reduction of this derivative 11 afforded allyl O-(2,3-di-O-acetyl-6-O-benzoyl-4-deoxy-α-D-glucopyranosyl)-(1→4)-2,3,6-tri-O-acetyl-β-D-glucopyranoside (14), which was deallylated, activated as an trichloroacetimidate, and coupled to 2,3-di-O-benzyl-4,6-O-benzylidene-α-D-glucopyranosyl 2′,3′,6′-tri-O-benzyl-α-D-glucopyranoside (20). Several compounds were fully characterized by ¹H NMR spectroscopy. Deprotection furnished the monodeoxygenated tetrasaccharides 9 and 23.     

Influence of the Type of Junction in DNA-3′-Peptide Nucleic Acid (PNA) Chimeras on Their Binding Affinity to DNA and RNA

The automated on-line synthesis of DNA-3′-PNA (PNA=Polyamide Nucleic Acids) chimeras 1 – 3 is described, in which the 3′-terminal part of the oligonucleotide is linked to the aminoterminal part of the PNA either via a N-(2-mercaptoethyl)- (X=S), a N-(2-hydroxyethyl)- (X=O), or a N-(2-aminoethyl)- (X=NH) N-[(thymin-1-yl)acetyl]glycine unit. Furthermore, the DNA-3′-PNA chimera 4 without a nucleobase at the linking unit was prepared. The binding affinities of all chimeras were directly compared by determining their T_m values in the duplex with complementary DNA, RNA, or DNA containing a mismatch or abasic site opposite to the linker unit. We found that all investigated chimeras with a nucleobase at the junction form more stable duplexes with complementary DNA and RNA than the corresponding unmodified DNA. The influence of X on duplex stabilization was determined to be in the order O>S≈NH, rendering the phosphodiester bridge the most favored linkage at the DNA/PNA junction. The observed strong duplex-destabilizing effects, when base mismatches or non-basic sites were introduced opposite to the nucleobase at the DNA/PNA junction, suggest that the base at the linking unit contributes significantly to duplex stabilization.     

The structure characterization of dinucleoside and nucleoside glucopyranosides lipophilic phosphotriesters by fast-atom bombardment tandem mass spectrometry

Rules for the gas-phase fragmentation mechanism of the negative ions of lipophilic phosphotriester molecules of biological interest have been established by fast-atom bombardment mass spectrometry/mass spectrometry. The mass-analyzed ion kinetic energy spectra of the [M ? H]^? of dinucleoside (1–4) and nucleoside glucopyranoside (5–9) phosphotriesters show that in the absence of charges on the phosphate bridge, the availability of acidic protons on the 5′-end nucleobase drives a preferred reaction path which leads to 5′-O-nucleotide or 6-O-glucopyranoside monophosphate anions.     

Catalytic enantioselective reactions. Part 18: Preparation of 3-deoxy-3-N,N-dialkylamino-1,2;5,6-di-O-isopropylidene-d-altritol derivatives from d-mannitol and their applications for catalytic enantioselective addition of dialkylzinc to aldehydes

A series of new chiral β-aminoalcohols, 3-deoxy-3-N,N-dialkylamino-1,2;5,6-di-O-isopropylidene-d-altritol derivatives 2–4 possessing a variety of amine substituents at the 3-position and thiol or acetylthio group at the 4-position was prepared from d-mannitol and enantioselective additions of diethylzinc to aldehydes using them as chiral catalysts were examined.     

Synthesis of oligoribonucleotides containing isoguanosine

Oligoribonucleotides containing isoguanosine ( ? 1,2-dihydro-2-oxoadenosine; isoG; 1 ) were prepared. The building block 2 was synthesized using the (dimethylamino)methylidene residue as NH₂ protecting group. The monomethoxytrityl as well as dimethoxytrityl group were introduced at OH–C(5′) (→ 5 and 6 ). Silylation of 5 with triisopropylsilyl chloride formed the 2′-O-blocked derivative 7 almost exclusively. Reaction with PCl₃/1,2,4-1H-triazole furnished the phosphonate 2 which was used in solid-phase synthesis of the oligoribonucleotides 10 and 11 . RNAse T₁ hydrolyzed U-A-G-U-U-isoG-U-U-A-G ( 10 ) at the 3′-site of G but not of isoG. The self-complementary oligomer (A-U-isoG-U)₃ ( 11 ) formed a duplex which was less stable than that of (A-U)₆.     

Synthesis and transformations of 3-allyl-7,10-dimethyl-2-sulfanylidene-2,3,5,6-tetrahydrospiro[benzo[<Emphasis Type="Italic">h</Emphasis>]quinazoline-5,1′-cyclopentan]-4(1<Emphasis Type="Italic">H</Emphasis>)-one

Ethyl 4′-amino-5′,8′-dimethyl-1′H-spiro[cyclopentane-1,2′-naphthalene]-3′-carboxylate reacted with allyl isothiocyanate to give 3-allyl-7,10-dimethyl-2-sulfanylidene-2,3,5,6-tetrahydrospiro[benzo[h]quinazoline- 5,1′-cyclopentan]-4(1H)-one. Reactions of the latter with alkyl halides and hydrazine hydrate and subsequent transformations of the products afforded a series of new benzo[h]quinazoline derivatives containing an allyl group in the 3-position.     

Discrimination of carbonyl groups of meso-α-diketones with Horner-Wadsworth-Emmons reagent of chiral binaphthyl esters

Asymmetric Horner-Wadsworth-Emmons reactions of selected meso-α-dicarbonyl compounds with chiral phosphonate reagents, which possessed axially dissymmetric 1,1′-bi-2- or 8-naphthol at the carboxylate moiety as a chiral auxiliary, were examined. The reactions proceeded smoothly with good chemical yields as well as with high diastereoselectivities. Z-olefins were preferentially formed, and it was found that the free hydroxy group at the 2′- or 8′-position on the naphthalene ring plays a crucial role in the high diastereoselectivity, probably due to a complex-induced proximity effect. Mechanistic considerations are also described.     

One-pot carbanionic access to methylenebis(phosphonate) analogues of natural P,P-glycosyl-disubstituted pyrophosphates

Two novel lithiated carbanions derived from ethyl (1,2:3,4-diisopropylidene-α-d-galactopyranosyl) methyl phosphonate 3a and ethyl (1-O-methyl-2,3-O-isopropylidene-β-d-ribofuranosyl) methylphosphonate 3b were used in the one-pot alkylidene diphosphorylation of 2,3-O-isopropylidene uridine or 2,3:5,6-di-O-isopropylidene-d-mannofuranose to synthesise the methylenebis(phosphonate) analogues of natural P¹,P²-glycosyl-disubstituted pyrophosphates.     

New Salt Spiropyran of Indoline Series with Fluorine Substituent

Synthesis, study of structure and photochromic properties of new salt spiropyran of indoline series containing a fluorine substituent in the 6′-position of the 2H-chromene moiety have been described in the work. The structure of the compound has been confirmed by ¹H NMR spectroscopy and X-ray diffraction analysis. Comparison of the structure of the compound with the previously studied analogue containing a methyl group instead of a fluorine atom in the 6′-position of the [2H]-chromene moiety has been made. This compound has been found to be photochromic, long-wavelength absorption maximum of its open form shows a bathochromic shift, and lifetime is increased three times as compared with the methyl analogue.     

Synthesis of 8-aryl-3,5,7,3′,4′-penta-O-methylcyanidins from the corresponding quercetin derivatives by reduction with LiAlH4

Synthesis of 8-aryl-3,5,7,3′,4′-penta-O-methylcyanidins from the corresponding quercetin derivatives by reduction with LiAlH₄ is reported. Regioselective iodination at the 8-position of penta-O-methylquercetin followed by a Suzuki-Miyaura reaction gave the 8-arylated quercetin derivatives. By the reduction of 8-arylated quercetins using 4 equiv. of LiAlH₄ at room temperature for 30 min, the corresponding anthocyanidins were obtained with a good yield.     

Synthesis of new nucleoside analogs containing amino bisphosphonic groups

Adenosine derivatives containing a 2,2-bis(diethoxyphosphoryl)ethyl or 2,2-diphosphonoethyl group on the amino nitrogen atom were synthesized for the first time by reaction of 5′-chloro-5′-deoxy- and 5′-hydroxy-2′,3′-isopropylideneadenosine with tetraethyl ethene-1,1-diylbis(phosphonate) or tetrakis(trimethylsilyl) ethene-1,1-diylbis(phosphonate).     

Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides

Model 3′-azido-3′-deoxynucleosides with thiol or vicinal dithiol substituents at C2′ or C5′ were synthesized to study reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides. Esterification of 5′-(tert-butyldiphenylsilyl)-3′-azido-3′-deoxyadenosine and 3′-azido-3′-deoxythymidine (AZT) with 2,3-S-isopropylidene-2,3-dimercaptopropanoic acid or N-Boc-S-trityl-L-cysteine and deprotection gave 3′-azido-3′-deoxy-2′-O-(2,3-dimercaptopropanoyl or cysteinyl)adenosine and the 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl or cysteinyl)thymidine analogs. Density functional calculations predicted that intramolecular reactions between generated thiyl radicals and an azido group on such model compounds would be exothermic by 33.6–41.2 kcal/mol and have low energy barriers of 10.4–13.5 kcal/mol. Reduction of the azido group occurred to give 3′-amino-3′-deoxythymidine, which was postulated to occur with thiyl radicals generated by treatment of 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl)thymidine with 2,2′-azobis-(2-methyl-2-propionamidine) dihydrochloride. Gamma radiolysis of N₂O-saturated aqueous solutions of AZT and cysteine produced 3′-amino-3′-deoxythymidine and thymine most likely by both radical and ionic processes.     

7‐De­aza‐2′‐deoxy‐7‐propynyl­guanosine

The title compound, C₁₄H₁₆N₄O₄, adopts the anti conformation at the gly­cosylic bond [χ−117.1 (5)°]. The sugar pucker of the 2′‐deoxy­ribo­furan­osyl moiety is C2′‐endo–C3′‐exo, ²T₃ (S‐type). The orientation of the exocyclic C4′—C5′ bond is +sc (gauche). The propynyl group is linear and coplanar with the nucleobase moiety. The structure of the compound is stabilized by several hydrogen bonds (N—H⋯O and O—H⋯O), leading to the formation of a multi‐layered network. The nucleobases, as well as the propynyl groups, are stacked. This stacking might cause the extraordinary stability of DNA duplexes containing this compound.     

γ-Radiolysis of 2′-deoxy-5-fluorouridine derivatives with sulfur-containing substituents

2′-Deoxy-5-fluorouridine (5-FUdR) derivatives having various types of sulfur-containing substituents at the 5′-O-position were synthesized and their γ-radiolyses were studied in aqueous solutions. The γ-radiolysis of compounds having 1,3-dithiol-2-yl and 1,3-dithian-2-yl substituents at the 5′-O-position efficiently gave 5-FUdR, specifically via the attack of hydroxyl radical. On the other hand, the γ-radiolysis of a compound having a sulfonylmethyl substituent at the 5′-O-position gave less efficiently 5-FUdR, specifically via the attack of the hydrated electron. The mechanistic features of these reactions are discussed.     

Nucleotides. Part LIV. Synthesis of condensed N1-(2′-deoxy-β-D-ribofuranosyl)lumazines,New fluorescent building blocks in oligonucleotide synthesis

Various condensed areno[g]lumazine derivatives 2 , 3 , and 5 – 7 were synthesized as new fluorescent aglycones for glycosylation reactions with 2-deoxy-3, 5-di-O-(p-toluoyl)-α/β-D -erythro-pentofuranosyl chloride ( 10 ) to form, in a Hilbert-Johnson-Birkofer reaction, the corresponding N¹-(2′-deoxyribonucleosides) 15 – 21 . The β-D -anomers 15 , 17 , 19 , and 21 were deblocked to 24 – 27 and, together with N¹-(2′-deoxy-β-D -ribofuranosyl)lumazine ( 22 ) and its 6, 7-diphenyl derivative 23 , dimethoxytritylated in 5′-position to 28–33. These intermediates were then converted into the 3′-(2-cyanoethyI diisopropylphosphoramidites) 34 – 39 which function as monomeric building block in oligonucleotide syntheses as well as into the 3′-(hydrogen succinates) 40 – 45 which can be used for coupling with the solid-support material. A series of lumazine-modified oligonucleotides were synthesized and the influence of the new nucleobases on the stability of duplex formation studied by measuring the T_m values in comparison to model sequences. A substantial increase in the T_m is observed on introduction of areno[g]lumazine moieties in the oligonucleotide chain stabilizing obviously the helical structures by improved stacking effects. Stabilization is strongly dependent on the site of the modified nucleobase in the chain.     

Dinucleotides containing two allyl groups by combinations of allyl phosphotriesters, 5-allyl-, 2′-O-allyl- and 2′-arabino-O-allyl uridine derivatives as substrates for ring-closing metathesis

Five different dinucleotides, each containing two allyl groups in various positions, were prepared and studied as substrates for ring-closing metathesis reactions. These dinucleotides were designed from appropriate nucleoside building blocks combining four different positions for the allyl group; the allyl phosphotriester linkage, 5-allyl-2′-deoxyuridine, and ribo- as well as arabino-configured 2′-O-allyluridine. Thus, convenient procedures for these building blocks were developed. From the dinucleotides, two new cyclic nucleotide structures were obtained; one connecting two adjacent nucleobase moieties and the other forming an unsaturated four-carbon linkage between the phosphate moiety and the adjacent pyrimidine nucleobase. The latter cyclic dinucleotide was also prepared with a saturated four-carbon linkage using a tandem ring-closing metathesis-hydrogenation procedure. This compound was found to be significantly more stable towards a nucleophilic ring-opening than its unsaturated counterpart.