Design, synthesis, and evaluation of a novel bridged nucleic acid, 2′,5′-BNA, with S-type sugar conformation fixed by N-O linkage

We designed a novel 2′-O,5′-N bridged nucleic acid, 2′,5′-BNA^ON, whose sugar puckering was fixed to S-type conformation by an N-O linkage. A dimer unit formed from 2′,5′-BNA^ON-U and thymidine was synthesized via a coupling reaction between a protected 2′,5′-BNA^ON-U monomer and a thymidine derivative. Introduction of 2′,5′-BNA^ON-U into DNA was carried out using conventional phosphoramidite chemistry with a DNA synthesizer. The hybridization abilities of 2′,5′-BNA^ON-U-modified oligonucleotides against DNA or RNA complement were evaluated.     

Synthesis and conformation of a novel bridged nucleic acid having a trans-fused 3,5,8-trioxabicyclo[5.3.0]decane structure

A novel bridged nucleic acid analogue, 2′-deoxy-trans-3′,4′-BNA thymine monomer, was successfully synthesized. An ab initio calculation and X-ray structure analysis revealed that the trans-fused bicyclo[5.3.0]decane structure of the 2′-deoxy-trans-3′,4′-BNA effectively constrained the sugar puckering in C_2^′-endo with appropriate γ, δ and χ angles.     

Development of a novel nucleoside analogue with S-type sugar conformation: 2′-deoxy-trans-3′,4′-bridged nucleic acids

Two novel trans-3′,4′-bridged nucleic acid (trans-3′,4′-BNA) monomers, one with a 3,5,8-trioxabicyclo[5.3.0]decane structure and the other with a 4,7-dioxabicyclo[4.3.0]nonane structure, were successfully synthesized from thymidine. The locked trans-fused ring structures of the nucleoside analogues were confirmed by X-ray crystallography, which also indicated that their furanose rings had a typical S-type conformation involving C_2′-endo or C_3′-exo sugar puckering, respectively, and the same ring conformation as that observed in the B-type helical structure of the DNA duplex.     

Reaction of 1-substituted 3-aminoquinoline-2,4-diones with isothiocyanates. An easy pathway to generate novel 2-thioxo-1′H-spiro[imidazoline-5,3′-indole]-2,2′-diones

3-Butyl-3-amino-1H,3H-quinoline-2,4-diones react with isothiocyanates to give novel 3a-butyl-9b-hydroxy-2-thioxo-1,2,3,3a,5,9b-hexahydro-imidazo[4,5-c]quinolin-2-ones in high yields. These compounds rearrange in boiling acetic acid or concd hydrochloric acid to give (E)- and/or (Z)-4-butylidene-2-thioxo-1′H-spiro[imidazoline-5,3′-indole]-2,2′-diones. All compounds were characterized by their ¹H, ¹³C, IR and MS spectra, and some of them also by ¹⁵N NMR. The structure of one compound was investigated by single-crystal X-ray diffraction.     

Synthesis of a series of novel 2′,3′-dideoxy-6′,6′-difluoro-3′-thionucleosides

A series of novel 2′,3′-dideoxy-6′,6′-difluoro-3′-thionucleosides 1a-d, analogues of 3TC that has high biological activities against HIV and HBV, have been synthesized from the gem-difluorohomoallyl amine 7 in a straightforward fashion. Our synthesis featured the construction of thiofuranose skeleton through ring closure of key intermediates and installation of pyrimidine ring with amino group in compounds 13a,b.     

Concise and efficient synthesis of 3′-O-triphosphates of 2′-deoxyadenosine and 2′-deoxycytidine

We describe concise and efficient synthesis of 2′-deoxyadenosine-3′-O-triphosphate (2′-d-3′-ATP) and 2′-deoxycytidine-3′-O-triphosphate (2′-d-3′-CTP) which are well known for their various biological applications. One-pot synthetic methodology was used to convert N⁶-Benzoyl-5′-O-levulinoyl-2′-deoxyadenosine into N⁶-Benzoyl-5′-O-levulinoyl-2′-deoxyadenosine-3′-O-triphosphate in 72% yield. One-step concurrent deprotection of N⁶-Benzoyl and 5′-O-levulinoyl groups using concentrated aqueous ammonia resulted in 2′-d-3′-ATP in 75% yield. The same synthetic strategy was successfully employed to convert N⁴-Benzoyl-5′-O-levulinoyl-2′-deoxycytidine into 2′-d-3′-CTP in 66% yield.     

Diastereoselective synthesis of 1-alkyl-2,4,6-trioxoperhydropyrimidine-5-spiro-3′-(1′,2′,3′,4′-tetrahydroquinolines)

Knoevenagel products formed by the condensation of N-monoalkyl barbituric acids with o-tert-amino benzaldehydes undergo tert-amino effect reactions (T-reactions) yielding 1-alkyl-2,4,6-trioxoperhydropyrimidine-5-spiro-3′-(1′,2′,3′,4′-tetrahydroquinoline) derivatives as a mixture of (S^∗,S^∗)- and (S^∗,R^∗)-diastereomers. Mostly, the major diastereomer has the S^∗,S^∗-configuration. According to X-ray diffraction data in the solid form and NOE data in solution, diastereoselectivity of the T-reactions can be associated with the structure of the Knoevenagel products whose conformation is fixed by the strong intramolecular C-H?π interaction.     

Straightforward synthesis of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes via 2′,3′-O-orthoester group elimination: a simple route to 3′,4′-didehydronucleosides

Straightforward, high-yielding syntheses of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes and 3′-deoxy-3′,4′-didehydronucleosides starting from 2′,3′-O-orthoester derivatives of ribonucleosides are described.     

5′-Epimeric 3′-deoxy-3′,4′-didehydronucleoside-5′-C-phosphonates: synthesis and structural assignment by NMR and X-ray analyses

Epimeric 5′-(RS) dialkyl 3′-deoxy-3′,4′-didehydro-5′-C-phosphonates were prepared by nucleophilic addition of various dialkyl phosphites to 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes. Whereas direct NMR configuration assignment for the C5′ atom bearing the phosphoryl and hydroxy groups using the J (P,H4′) and J (H5′,H4′) coupling constants is impossible due to the absence of the H4′ atom, successful separation, crystallisation and X-ray crystallographic analysis of a pair of epimeric 5′-C-phosphonates, followed by correlation with a series of NMR parameters, led to efficacious configuration assignment of individual epimers in the mixtures.     

One stone kills four birds: a novel diazaperinone 12H-pyrazino[2′,3′:3,4]pyrrolo[1,2-a]perimidin-12-one recognizes four different metal ions

A novel diazaperinone 12H-pyrazino[2′,3′:3,4]pyrrolo[1,2-a]perimidin-12-one has been successfully synthesized through a one-step condensation. Single crystal X-ray analysis shows that the product is of planar structure with strong π?π interactions and H-bonding. Interestingly, the 12H-pyrazino[2′,3′:3,4]pyrrolo[1,2-a]perimidin-12-one can recognize three different metal cations Cu²⁺, Ag⁺ and Hg²⁺ via naked eye visualization, and shows turn-on fluorescence for Fe³⁺ and Ag⁺ among the 22 metal cations.     

On the design of polymeric 5′-O-ester prodrugs of 3′-azido-2′,3′-dideoxythymidine (AZT)

A new 5′-O-AZT prodrug was synthesized by conjugating 3′-azido-2′,3′-dideoxythymidine (AZT) with poly(oxyethylene H-phosphonate) at room temperature under Atherton-Todd reaction conditions. The acute toxicity of poly(5′-O-AZT-oxyethylene phosphate) was reduced significantly in comparison with non-immobilized AZT.     

Convenient synthesis of N-isobutyryl-2′-O-methyl guanosine by efficient alkylation of O-trimethylsilylethyl-3′,5′-di-tert-butylsilanediyl guanosine

We present a novel route for the synthesis of N²-isobutyryl-2′-O-methyl guanosine, introducing 3′,5′-di-tert-butylsilyl and O⁶-trimethylsilylethyl groups as efficient protections during the 2′-O-methylation step with NaH/CH₃I. These protections were then removed simultaneously in a single step with TBAF. The eight-step synthesis is easy to perform, employing convenient commercially available reagents; crude mixtures are of satisfying purity, so only three chromatography purifications were required. Title compound was obtained in 25% overall yield from guanosine.     

Cyclization versus oligomerization of SP- and RP-5′-OH-N-benzoyl-2′-deoxycytidine-3′-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane)s

The S_P-isomer of 5′-OH-N⁴-benzoyl-2′-deoxycytidine-3′-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) undergoes DBU-promoted intramolecular cyclization providing as a sole product S_P-deoxycytidine cyclic 3′,5′-O,O-phosphorothioate. Unexpectedly, the R_P-counterpart yields a mixture of products consisting of R_P-deoxycytidine cyclic 3′,5′-O,O-phosphorothioate and macrocyclic oligo(deoxycytidine phosphorothioate)s. The results of molecular modeling indicate that the dychotomy observed for the R_P substrate may result from remarkably higher energy of the corresponding transition states, caused by the presence of bulky ‘spiro’ pentamethylene substituent at the position C4 in the oxathiaphospholane ring.     

A convenient synthesis of the cytidyl 3′-terminal monomer for solid-phase synthesis of RNG oligonucleotides

Replacing the phosphodiester backbone of RNA with positively charged guanidinium linkages has been shown to enable RNA oligomers to overcome electrostatic repulsion and bind double-stranded DNA in a triplex with high affinity. Ribonucleotide monomers with the ability to form guanidinium linkages have been synthesized for the generation of ribooligonucleotides with guanidinium linkages (RNGs) through solid-phase synthesis. We report herein an efficient method for the synthesis of N⁴-benzoyl-2′-O-(tert-butyldimethylsilyl)-5′-N-(4-monomethoxytritylamino)-3′-O-succinyl-5′-deoxycytidine, a new monomer required for the solid-phase synthesis of cytidyl RNG oligonucleotides.     

New active ruthenium(II) complexes based N3,N3′-bis(diphenylphosphino)-2,2′-bipyridine-3,3′-diamine and P,P′-diphenylphosphinous acid-P,P′-[2,2′-bipyridine]-3,3′-diyl ester ligands for transfer hydrogenation of aromatic ketones by propan-2-ol

The dimeric starting material [Ru(η⁶-p-cymene)(μ-Cl)Cl]₂ reacts with N3,N3′-bis(diphenylphosphino)-2,2′-bipyridine-3,3′-diamine, 1 and P,P′-diphenylphosphinous acid-P,P′-[2,2′-bipyridine]-3,3′-diyl ester, 2 ligands to afford bridged dinuclear complexes [C₁₀H₆N₂{NHPPh₂-Ru(η⁶-p-cymene)Cl₂}₂], 3 and [C₁₀H₆N₂{OPPh₂-Ru(η⁶-p-cymene)Cl₂}₂], 4 in quantitative yields. These bis(aminophosphine) and bis(phosphinite) based Ru(II) complexes serve as active catalyst precursors for the transfer hydrogenation of acetophenone derivatives in 2-propanol and especially 4 acts as a good catalyst, giving the corresponding alcohols in 99% yield in 20 min (TOF ? 280 h⁻¹).     

N-Alkyl- and N-aryl-dithieno[3,2-b:2′,3′-d]pyrrole-containing organic dyes for efficient dye-sensitized solar cells

Two new organic sensitizers, 2-cyano-3-(6-(4-(diphenylamino)phenyl)-4-(2-ethylhexyl)-4H-dithieno[3,2-b:2′,3′-d]pyrrol-2-yl)acrylic acid and 2-cyano-3-(6-(4-(diphenylamino)phenyl)-4-(4-(hexyloxy)phenyl)-4H-dithieno[3,2-b:2′,3′-d]pyrrol-2-yl)acrylic acid, consisting of electron donating (triphenylamine) and electron accepting (cyanoacrylic acid) functionalities linked by two different rigidified π-spacers, N-alkyl- and N-aryl-dithieno[3,2-b:2′,3′-d]pyrrole, were designed, synthesized and applied for dye-sensitized solar cells, respectively. The materials were successfully synthesized through Knoevenagel condensation reactions. Ultraviolet–visible absorption spectra revealed that the use of either of rigidified π-spacer resulted in similar charge transfer transition, however, enhanced spectral response was observed when compared with an oligothiophene analogue. In terms of their photovoltaic performance, new dyes outperformed the reference bithiophene sensitizer when tested with nitrile-based and ionic liquid-based electrolytes.     

The preparation of substituted bithiophenyl aldehydes via the ring opening of dithieno[2,3-b:3′,2′-d]thiophene in the presence of n-BuLi

In the presence of n-BuLi in THF at low temperature, the phenomena of ring opening of symmetric substituted dithieno[2,3-b:3′,2′-d]thiophenes were observed. After quenching the organolithium intermediates with dry DMF, a series of substituted novel bithiophenyl aldehydes were prepared in good to excellent yields. The mechanism shows the key step for the ring opening of dithieno[2,3-b:3′,2′-d]thiophene is the nucleophilic attack of butyl anion onto the sulfur atom of the central ring. Total ten samples of symmetric substituted dithieno[2,3-b:3′,2′-d]thiophenes and their ring-opened products, the substituted bithiophenyl aldehydes were characterized by ¹H NMR, ¹³C NMR, and HRMS. Two ring-opened products were confirmed by X-ray single crystal analysis.     

Synthesis of hapten-phosphoramidites from 2′-deoxyuridine

A total of 11 novel phosphoramidites, 3a-d, 4a-d and 14a-c were prepared from 2′-deoxyuridine functionalized at 5 and 6-position of the pyrimidine ring with hapten reporter groups, e.g. adamantane, carbazole, dansyl and dabsyl, suitable for use in immunodetection nucleic acid testing assays.     

Application and details of photoinduced oxidative cyclization of 5-(4′,9′-methanocycloundeca-2′,4′,6′,8′,10′-pentaenylidene)pyrimidine-2,4,6(1,3,5H)-triones and related compounds

As novel methodology for synthesizing the furan ring, a photoinduced oxidative cyclization of 5-(4′,9′-methanocycloundeca-2′,4′,6′,8′,10′-pentaenylidene)pyrimidine-2,4,6(1,3,5H)-triones (7a-c) and related compounds 9a-c was accomplished to give 5,10-methanocycloundeca[4,5]furo[2,3-d]pyrimidine-2,4(1,3H)-dionylium tetrafluoroborates (8a-c⁺·BF₄⁻) and related compounds 2a-c⁺·BF₄⁻, respectively. In the photoinduced oxidative cyclization, the molecular oxygen in air is used as oxidant and the reaction proceeds under mild conditions to give desired products without byproducts, and thus, it is interesting from the viewpoint of the green chemistry. On the reactions of the mono-substituted derivatives 7d,e and 9e,f, the selectivity of the photoinduced cyclizations were reversed as compared with those of the DDQ-promoted oxidative cyclizations. By the NMR monitoring of the reactions of 7a and deuterated compound 7a-D₂ under degassed conditions, the details of the reaction pathway were clarified and rationalized on the basis of the MO calculation by the 6-31G^∗ basis set of the MP2 levels as well.     

Synthesis of 2′,3′-dideoxy-6′,6′-difluoro-3′-azanucleosides

The straightforward synthesis of four novel 2′,3′-dideoxy-6′,6′-difluoro-3′-azanucleosides 1a-d is described. Efficient construction of the fluorine-containing pyrrolidine ring through two different ways and installation of pyrimidine rings using the amino groups in the intermediates 12, 26 were the key steps of our synthesis.