Oligoribonucleotides containing an aminoalkyl group at the N(4) atom of cytosine as precursors of new reagents for site-specific modifications of biopolymers

A solid-phase H-phosphonate procedure was developed for the synthesis of oligoribonucleotides containing aliphatic amino linkers with different lengths at the N(4) atom of cytosine. The hybridization properties of modified oligoribonucleotides were studied. Thermal stability of the RNA—RNA* and DNA—RNA* duplexes depends on the position of modified cytosine in the chain and the type of the duplex.     

The Synthesis and Mechanistic Considerations of a Series of Ammonium Monosubstituted H-Phosphonate Salts

A series of ammonium monosubstituted H-phosphonate salts were synthesized by combining H-phosphonate diesters with amines in the absence of solvent at 80 °C. Variation of the ester substituent and amine produced a range of ionic liquids with low melting points. The products and by-products were analyzed by spectroscopic and spectrometric techniques in order to get a better mechanistic picture of the dealkylation and formal dearylation observed. For dialkyl H-phosphonate diesters, (RO)₂P(O)H (R=alkyl), the reaction proceeds via direct dealkylation with the reactivity increasing in the order R=iPr<Et<Me corresponding to DFT calculated activation enthalpies of 22.6, 20.8, and 17.9 kcal mol⁻¹. For the diphenyl H-phosphonate diesters, (PhO)₂P(O)H, the dearylation was found to proceed via phenol-assisted formation of a 5-coordinate intermediate, (PhO)₃PH(OH), from which P(OPh)₃ and water were eliminated. The presence of an equivalent of water then facilitated the formation of P(OH)₂OPh and the amine, R'NH₂, subsequently abstracted a proton from it to yield [(PhO)PH(O)O]^-[R'NH₃]⁺.     

Microwave Induced Reaction of H-Dimethylphosphonate with Styrene Oxide

Microwave catalyzed reaction of a neat mixture of styrene oxide and H-dimethylphosphonate furnished dimethyl methylphosphonate, trimethylphosphate, phenylacetaldehyde, 1-methoxy-2-phenylethanol, 1-phenylethleneglycol, cis- and trans-1,3-diphenylcyclobutanes, hydrogen 1-(2-phenylethyl)methylphosphinate, (1-phenylethyl)dimethylphosphonate, and (1-phenylethyl)dimethylphosphonate via free radical processes.     

Efficient preparation of amine-modified oligodeoxynucleotide using modified H-phosphonate chemistry for DNA microarray fabrication

Amine-modified oligodeoxynucleotides (AMO) are commonly used probe oligodeoxynucleotides for DNA microarray preparation. Two methods are currently used for AMO preparation—use of amine phosphoramidites protected by acid-labile monomethoxytrityl (MMT) groups or alkali-labile trifluoroacetyl (TFA) groups. Because conventional AMO preparation procedures have defects, for example stringent acidic conditions are required for deprotection of MMT and hydrophobic purification cannot be used for TFA-protected amino groups, conventional preparation of AMO is unlikely to result in the expected outcome. In this paper a method of AMO synthesis using modified H-phosphonate chemistry is suggested. An aliphatic diamine is coupled with a phosphonate group forming a phosphoramidate linkage to the last internucleotide phosphate of oligodeoxynucleotides. In this method dimethoxytrityl (DMT) purification steps are used and stringent acid deprotection is not required to obtain the AMO. Although the method could lead to formation of AMO diastereomers, melting-temperature and CD analysis showed for two AMO that DNA duplex formation was the same as when normal oligodeoxynucleotides were used. Also, when these AMO were used as probes for DNA microarrays the immobilization efficiency was similar to that for AMO probes prepared by conventional means using an amino-modifier unit. The hybridization performance of these AMO was better than for those prepared conventionally. The procedures suggested would be useful for preparation of efficient AMO for fabrication of DNA microarrays and DNA-based nanoparticle systems. Nagendra Kumar Kamisetty and Seung Pil Pack have equally contributed to this work.     

Synthesis of N-Phosphoryl Branched Peptides

H-phosphonates were conveniently prepared by direct transesterification of diphenyl phosphite (DPP) with the corresponding alcohols, without further purification they were reacted with branched peptide methyl ester (L-Leu2-L-LysOMe) through Atherton-Todd method, a series of different substituted alkyloxy (N-phosphoryl-L-Leu)2-L-LysOMe were synthesized, and their stmctures were confirmed by ^31P NMR, ESI-MS, ^1H NMR, ^13C NMR, IR and elemental analysis. The approach possesses the advantages of easy operation, high yield and inexpensive phosphorylating reagent.     

Novel benzyl rearrangements in electrospray ionization multistage tandem mass spectra of benzyl 2',3'- didehydro-2',3'-dideoxythymidin-5'-yl H-phosphonate

Several alkyl 2',3'-didehydro-2',3'-dideoxythymidin-5'-yl H-phosphonates were synthesized and analyzed by electrospray ionization multistage tandem mass spectrometry (ESI-MS(n)). Two kinds of novel benzyl rearrangement reactions were observed in ESI - MS(2) of [M + H](+), [M + Na](+) and [M + K](+) of benzyl 2',3'-didehydro-2',3'-dideoxythymidin-5' yl H-phosphonate. Results from tandem mass spectrometry, high-resolution mass spectrometry and control experiments showed that the benzyl migration could undergo a four-membered cyclic rearrangement reaction, and benzyl was essential in the process.     

Microwave-Assisted Reaction of Dimethyl H-Phosphonate with Cyclohexene and Alkene Oxides

Microwave-assisted reaction of dimethyl H-phosphonate with cyclohexene-, 1,2-butene-, and 1,2-decene oxides furnishes 8, 5, and 17 compounds, respectively. The probable mechanism of the formation of the various compounds via free radical reactions and their GC-MS characterization are presented in this article.     

First synthesis of natural phosphatidyl-β-d-glucoside

Herein, we report the chemical synthesis of naturally occurring mammalian phosphatidyl-β-d-glucoside (PtdGlc), in order to confirm the proposed structure and to clarify its stereochemistry. We designed a convergent synthetic strategy, suitable to prepare sensitive PtdGlc derivatives. As an initial demonstration of our strategy, we successfully prepared both PtdGlc diastereomers as well as its sensitive arachidonyl analogue. The presence of both diastereomers in the natural sample was confirmed.     

Novel and Convenient Approach to Synthesis of AZT／d4T H-phosphonates

A convenient, efficient and general method has been developed for synthesis of H-phosphonate mono and diesters of AZT and d4T through one-pot reaction of phosphonic acid with AZT or d4T and different alcohols using pivaloyl chloride as condensing agent under mild conditions.