A versatile reagent for the synthesis of 5′-phosphorylated, 5′-thiophosphorylated or 5′-phosphoramidate-conjugated oligonucleotides

We report the synthesis of a new phosphorylating reagent that is easily accessible and allows not only the chemical synthesis of 5′-phosphorylated and 5′-thiophosphorylated oligonucleotides but also the 5′-conjugation through a phosphoramidate linkage. 5′-Amino-linker and 5′-alkyne oligonucleotides were obtained and the latter was conjugated by a 1,3-dipolar cycloaddition (click chemistry) with a galactosylated azide derivative to afford 5′-galactosyl oligonucleotide with high efficiency.     

Simple reagent for the synthesis of oligonucleotides labeled with 3,3,3′,3′-tetramethyl-2,2′-indodicarbocyanine

Synthesis of a phosphoramidite reagent for the preparation of oligonucleotides labeled at the 5′-end with a fluorescent dye, 3,3,3′,3′-tetramethyl-2,2′-indodicarbocyanine, is described. The efficiency of this reagent is confirmed by the synthesis of several labeled oligonucleotides. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 154–158, January, 2006.     

New reagent for the preparation of oligonucleotides involving a 5′-thiophosphate or a 5′-phosphate group

We report here a novel, simple reagent enabling the chemical incorporation of a thiophosphate or a phosphate group at the 5′-end of oligonucleotides using very mild basic deprotection conditions. This method can be useful in the case of alkali sensitive modified oligonucleotides. This reagent also gives access to the preparation of bifunctional oligonucleotides with either a thiophosphate group at the 5′-end and a phosphate at the 3′-end, or two thiophosphate groups at both the 5′- and the 3′-ends, or a 5′-thiophosphate group and a 3′-amino-containing linker.     

Bromodimethylsulfonium bromide (BDMS)-catalyzed multicomponent synthesis of 3-aminoalkylated indoles

Bromodimethylsulfonium bromide (BDMS)-catalyzed three-component coupling reaction between indoles, aldehydes, and N-alkylanilines is reported to access substituted 3-aminoalkylated indoles at room temperature in high yields (82-96%) within 1.5-3.5 h. The salient features of this protocol are the simplicity of the procedure, the ready accessibility of the catalyst, its cost effectiveness, and higher yields in relatively short reaction times.     

First synthesis of 1,1-ferrocene bis-aminophosphonic esters

The series of aminophosphonates bearing the 1,1^′-bis-substituted ferrocenyl moiety was obtained by the addition of dialkyl phosphites to an azomethine bond of Schiff bases derived from 1,1^′-ferrocene-bis-carboxaldehyde. This addition led to both diastereoisomeric forms demonstrating its behaviour to be contrary to the addition to terephthalic Schiff bases, which led exclusively to a meso-form.     

A new protecting group ‘3,5-O-sulfinyl’ for xylo-nucleosides. A simple and efficient synthesis of 3-amino-3-deoxyadenosine (a puromycin intermediate), 2,2-anhydro-pyrimidine nucleosides and 2,3-anhydro-adenosine

We developed a new protecting group, the cyclic sulfite for the protection of the 3^′,5^′-dihydroxy group of nucleosides. Seven cyclic sulfites, 4a-c, 5a-b, and 6a-b were prepared in high yields from the corresponding xylo-uridines 1 and 2, and xylo-adenosines 3 with thionyl chloride, respectively. Synthesis of the puromycin intermediate 8 was carried out by deprotection of the sulfite moiety through an intramolecular cyclization of the 2^′-α-carbamate 7.     

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.     

Study on the synthesis of novel fluorescent macrocyclic sensors and their sensitive properties for Cu2+ and Fe3+ in aqueous solution

In this work, we synthesised and characterised three novel fluorescence macrocyclic sensors containing optically active dansyl groups. The studies for the interaction of the synthesised compounds with various mental ions (Li⁺, Na⁺, K⁺, Ag⁺, Mg²⁺, Ca²⁺, Ba²⁺, Pb²⁺, Zn²⁺, Co²⁺, Cd²⁺, Hg²⁺, Ni²⁺, Cu²⁺, Mn²⁺, Cr³⁺, Al³⁺, Fe³⁺) were performed by fluorescence titration, Job’s plot, ESI-MS and DFT calculations. The results showed that the sensors 1a–1c displayed selective recognition for Cu²⁺ and Fe³⁺ ions and formed stoichiometry 1:1 complex through PET mechanism in DMSO/H₂O solution (1:1, v/v, pH 7.4 of HEPES). The binding constant (K) and detection limit were calculated.     

A simple and stereodivergent strategy for the synthesis of 3′-C-branched 2′,3′-dideoxynucleosides exploiting (Z)-but-2-en-1,4-diol and (R)-2,3-cyclohexylideneglyceraldehyde

Barbier type additions of allylic bromide 4, derived from (Z)-but-2-en-1,4-diol 2 to (R)-2,3-cyclohexylideneglyceraldehyde 1 were performed through mediation with Zn employing Luche’s procedure and also with low valent Cu, Co, and Fe which were produced via bimetal redox strategy in THF to afford 5c,d as the major products. From these, 5a,b were prepared following an oxidation-reduction protocol. Compound 5c was exploited as a representative starting material to develop a simple and inexpensive strategy toward the synthesis of 3′-C-branched 2′,3′-dideoxynucleosides having stereodiversity at 3′- and 4′-positions.     

Efficient synthesis of orthogonally protected anti-2,3-diamino acids

An asymmetric synthesis of anti-2,3-diamino acids is reported. The enolates of N,N-dibenzylated β³-amino esters were treated with di-tert-butyl azodicarboxylate (DBAD) to afford their N′,N″-di-Boc-2-hydrazino derivatives with excellent anti diastereoisomeric ratio. Final Boc removal and reductive cleavage of the hydrazino bond led to the expected 2,3-diamino esters having only one free amino group. In comparison with other asymmetric C-2 amination procedures, this method does not need the use of expensive chiral reagents and/or chiral auxiliaries, while leads to products which can be orthogonally protected.     

A convenient one-pot three component synthesis of 3-aminoalkylated indoles catalyzed by 3-chlorophenylboronic acid

An efficient protocol was developed for the synthesis of 3-aminoalkylated indoles using 3-chlorophenylboronic acid as a catalyst under ambient temperature conditions. The three-component reaction of indoles, aromatic aldehydes and N-methyl aniline offered corresponding 3-aminoalkylated indoles in excellent yields. This protocol presents some remarkable features such as mild reaction conditions, simple workup procedure and excellent yields.     

An InCl3 catalyzed facile one-pot synthesis of novel dispiro[cyclopent-3′-ene]bisoxindoles

An InCl₃ catalyzed efficient synthesis of novel dispiro[cyclopent-3′-ene]bisoxindoles is accomplished via a one-pot reductive cyclization of isatylidene malononitriles using the Hantzsch ester.     

A novel Prins-alkynylation reaction for the synthesis of 4-phenacyl tetrahydropyrans

Aldehyde, homoallylic alcohol, and alkyne undergo smooth Prins-type cyclization in the presence of BF₃·OEt₂/CuCl (10 mol % each) in dichloromethane under mild reaction conditions to afford 4-phenacyl tetrahydropyran derivatives in good yields. This method is highly stereoselective, affording cis-tetrahydropyrans exclusively. The salient features of this method are high conversions, mild reaction conditions, short reaction times, high selectivity, and operational simplicity.     

A novel one-pot and efficient procedure for the synthesis of 3H-spiro[isobenzofuran-1,6′-pyrrolo[2,3-d]pyrimidine]-2′,3,4′,5′-tetraones

A novel and practical one-pot procedure is described for the preparation of several new of 3H-spiro[isobenzofuran-1,6′-pyrrolo[2,3-d]pyrimidine]-2′,3,4′,5′-tetraones based on the addition reaction of ninhydrin and 6-aminouracils followed by oxidative cleavage of their corresponding dihydroxyindenopyrrolopyrimidines.     

Fe3O4 nanoparticles: A powerful and magnetically recoverable catalyst for the synthesis of novel calix[4]resorcinarenes

A simple synthesis of novel and known calix[4]resorcinarenes derivatives has been achieved by the condensation of resorcinol and different aromatic aldehydes in the presence of catalytic amounts of Fe₃O₄ nanoparticles under solvent-free conditions.The experimental conditions have been thoroughly optimized and established,allowing significant rate enhancements and good to excellent yields.The reactions can be run safely without using any toxic organic solvents under mild reaction conditions.The Fe₃O₄ nanoparticles were characterized by powdered X-ray diffraction（XRD）,transmission electron microscopy（TEM） and FT-IR spectroscopy.     

A novel phosphoramidite method for automated synthesis of oligonucleotides on glass supports for biosensor development

Two protocols for functionalization of glass supports with hexaethylene glycol (HEG)-linked oligonucleotides were developed. The first method (standard amidite protocol) made use of the 2-cyanoethyl-phosphoramidite derivative of 4,4′-dimethoxytrityl-protected HEG. This was first coupled to the support by standard solid-phase phosphoramidite chemistry followed by extension with a thymidylic acid icosanucleotide. Stepwise addition of the linker phosphoramidite graduated at 1% (relative to the total sites available) perstep at 50°C resulted in an optimal yield of immobilized oligonucleotides at a density of 2.24 × 10¹⁰ strands/mm². This observed loading maximum lies well below the theoretical maximum loading owing to nonspecific adsorption of HEG on the glass and subsequent blocking of reactive sites. Surface loadings as high as 3.73 × 10¹⁰/mm² and of excellent sequence quality were achieved with a reverse amidite protocol. The support was first modified into a 2-cyanoethyl-N,N-diisopropylphosphoramidite analog followed by coupling with 4,4′-dimethoxytrityl-protected HEG. This protocol is conveniently available when using a conventional DNA synthesizer. The reverse amidite protocol allowed for control of the surface loading at values suitable for subsequent analytical applications that make use of immobilized oligonucleotides as probes for selective hybridization of sample nucleic acids of unknown sequence and concentration.     

Practical synthesis of adenosine 3′,5′-cyclic monophosphorodithioate

Adenosine 3′,5′-cyclic monophosphorodithioate (cAMPS₂), which has two exocyclic sulfurs directly attached to phosphorus, was synthesized from adenosine phosphoramidite by intramolecular cyclization employing the phosphotriester method as a key step.     

Preparation of the novel fluorine-18-labeled VIP analog for PET imaging studies using two different synthesis methods

Vasoactive intestinal peptide (VIP) receptors are expressed on various tumor cells in much higher density than somatostatin receptors, which provides the basis for radiolabeling VIP as tumor diagnostic agent. However, fast proteolytic degradation of VIP in vivo limits its clinical application. With the aim to develop and evaluate new ligands for depicting the VIP receptors with positron emission tomography (PET), the structure modified [R^8,15,21, L¹⁷]-VIP analog was radiolabeled with ¹⁸F using two different methods. With the first method, N-4-[¹⁸F]fluorobenzoyl-[R^8,15,21, L¹⁷]-VIP ([¹⁸F]FB-[R^8,15,21, L¹⁷]-VIP 7) was produced in a decay-corrected radiochemical yield (RCY) of 33.6 ± 3%, a specific radioactivity of 255 GBq/μmol (n = 5) within 100 min in four steps. Similarly, N-4-[¹⁸F](fluoromethyl)-benzoyl-[R^8,15,21, L¹⁷]-VIP ([¹⁸F]FMB-[R^8,15,21, L¹⁷]-VIP 8) was synthesized in a RCY of 34.85 ± 5%, a specific radioactivity of 180 GBq/μmol (n = 5) within 60 min in only one step. The two products 7 and 8 were both shown good stability in HSA. Moreover, the low bone uptakes of 7 and 8 in vivo of mice showed good defluorination stability.     

The synthesis, structure and reactivity of aldehyde substituted η-allylic complexes of molybdenum

Reaction of cis-[Mo(NCMe)₂(CO)₂(η⁵-L)][BF₄] (L=C₅H₅ or C₅Me₅) with 1-acetoxybuta-1,3-diene gives the cationic complexes [Mo{η⁴-syn-s-cis-CH₂CHCHCH(OAc)}(CO)₂(η⁵-L)][BF₄], which, on reaction with aqueous NaHCO₃/CH₂Cl₂, afford good yields of the anti-aldehyde substituted complexes [Mo{η³-exo-anti-CH₂CHCH(CHO)}(CO)₂(η⁵-L)] 2 (L=C₅Me₅), 4 (L=C₅H₅)]. The corresponding η⁵-indenyl substituted complex 5 was prepared by protonation (HBF₄·OEt₂) of [Mo(η³-C₃H₅)(CO)₂(η⁵-C₉H₇)] followed by addition of CH₂=CHCH=CH(OAc) and hydrolysis (aq. NaHCO₃/CH₂Cl₂). An X-ray crystallographic study of complex 2 confirmed the structure and showed that there is a contribution from a zwitterionic form involving donation of electron density from the molybdenum to the aldehyde carbonyl group. Treatment of 2 and 4, in methanol solution, with NaBH₄ afforded the alcohols [Mo{η³-exo-anti-CH₂CHCHCH₂(OH)}(CO)₂(η⁵-L)] [6 (L=C₅H₅), 8 (L=C₅Me₅)]; however, prolonged (30 h) reaction with NaBH₄/MeOH surprisingly gave good yields of the methoxy-substituted complexes [Mo{η³-exo-anti-CH₂CHCHCH₂(OMe)}(CO)₂(η⁵-L)] [7 (L=C₅H₅), 9 (L=C₅Me₅)], the structure of 7 being confirmed by single crystal X-ray crystallography. This methoxylation reaction can be explained by coordination of the hydroxyl group present in 6 and 8 onto B₂H₆ to form the potential leaving group HOBH₃⁻, which on ionisation affords [Mo(η⁴-exo-buta-1-3-diene)(CO)₂(η⁵-L)]⁺ which is captured by reaction with OMe⁻. Complex 8 is also formed in good yield on reaction of 2 with HBF₄·OEt₂ followed by treatment of the resulting cation [Mo{η⁴-exo-s-cis-syn-CH₂CHCHCH(OH)}(CO)₂(η⁵-C₅Me₅)][BF₄] with Na[BH₃CN]. Reaction of 4 with the Grignard reagents MeMgI, EtMgBr or PhMgCl afforded moderate yields of the alcohols [Mo{η³-exo-anti-CH₂CHCHCH(OH)R}(CO)₂(η⁵-C₅H₅)] [11 (R=Me), 12 (R=Et), 13 (R=Ph)]. Similarly, treatment of 2 with MeLi gave the corresponding alcohol 14. An attempt to carry out the Oppenauer oxidation [Al(OPr′)₃/Me₂CO] of 11 resulted in an elimination reaction and the formation of the η³-s-pentadienyl complex [Mo{η³-exo-anti-CH₂CHCH(CHCH₂)}(CO)₂(η⁵-C₅H₅)], which was structurally identified by X-ray crystallography. Interestingly, oxidation of 6 with [Bu₄ⁿN][RuO₄]/morpholine-N-oxide affords the aldehyde complex, 4 in good yield. Finally, reaction of 11 with [NO][BF₄] followed by addition of Na₂CO₃ affords the fur-3-ene complex [Mo{η²-

(H)Me}(CO)(NO)(η⁵-C₅H₅)].