Synthesis of alkylphosphon(othio)ate analogues of DNA

Solid-phase synthesis, thermal denaturation studies, nuclease resistance, and cellular uptake of (oligodeoxyribonucleoside)methylborane phosphine-DNA chimeras

The major hurdle associated with utilizing oligodeoxyribonucleotides for therapeutic purposes is their poor delivery into cells coupled with high nuclease susceptibility. In an attempt to combine the nonionic nature and high nuclease stability of the P-C bond of methylphosphonates with the high membrane permeability, low toxicity, and improved gene silencing ability of borane phosphonates, we have focused our research on the relatively unexplored methylborane phosphine (Me-P-BH(3)) modification. This Article describes the automated solid-phase synthesis of mixed-backbone oligodeoxynucleotides (ODNs) consisting of methylborane phosphine and phosphate or thiophosphate linkages (16-mers). Nuclease stability assays show that methylborane phosphine ODNs are highly resistant to 5' and 3' exonucleases. When hybridized to a complementary strand, the ODN:RNA duplex was more stable than its corresponding ODN:DNA duplex. The binding affinity of ODN:RNA duplex increased at lower salt concentration and approached that of a native DNA:RNA duplex under conditions close to physiological saline, indicating that the Me-P-BH(3) linkage is positively charged. Cellular uptake measurements indicate that these ODNs are efficiently taken up by cells even when the strand is 13% modified. Treatment of HeLa cells and WM-239A cells with fluorescently labeled ODNs shows significant cytoplasmic fluorescence when viewed under a microscope. Our results suggest that methylborane phosphine ODNs may prove very valuable as potential candidates in antisense research and RNAi.

Synthesis, resolution, and application of 2,2′-bis(diphenylphosphino)-3,3′-binaphtho[b]furan (BINAPFu)

(±)-2,2′-Bis(diphenylphosphino)-3,3′-binaphtho[2,1-b]furan (BINAPFu) was synthesized from 2-naphthoxyacetic acid in a five-step sequence in 62% overall yield. A variety of reported resolution procedures for biaryl bisphosphines did not work with (±)-BINAPFu; thus, a new resolution method was developed, involving the Staudinger reaction of the aforementioned racemate of BINAPFu with an enantiopure camphor sulfonyl azide derivative. The resulting diastereomeric phosphinimines were separated by flash chromatography. Subsequent hydrolysis to the corresponding bis-phosphine oxide and trichlorosilane reduction provided enantiopure BINAPFu. The absolute stereochemical configuration of BINAPFu was established by X-ray crystallography. BINAPFu was compared with commercially available 2,2′-bis(diphenylphosphino)-1,1′-binaphthalene (BINAP) in Pd(0)-catalyzed intermolecular Heck reactions. Investigation of the Heck arylation of 2,3-dihydrofuran showed BINAPFu to be more efficacious than BINAP in dioxane at 30 °C. A variety of phosphorus selenides were prepared, and the 1JP-Se coupling constants measured, to obtain a comparative scale of parent phosphine basicity. The phosphorus atoms in BINAPFu were found to be electron deficient when compared with BINAP but slightly more electron rich than trifurylphosphine. Key words: naphthofurans, atropisomers, electron-deficient phosphines, asymmetric Heck reactions, Staudinger reaction.

Synthesis and binding properties of oligodeoxynucleotides containing phenylphosphon(othio)ate linkages

A method for the synthesis of chimeric oligodeoxynucleotides comprised of phosphodiester and phenylphosphonate [3'-O-P(= O)(C6H5)-O-5'] or phenylphosphono-thioate [3'-O-P(= S)(C6H5)-O-5'] linkages has been developed. Synthesis was performed using suitably protected nucleoside phenylphosphonamidites as building blocks following an adjusted solid-phase phosphoramidite synthesis protocol. The new oligodeoxy-nucleotide analogues were characterized by electrospray ionization- and matrix-assisted laser desorption mass spectrometry, as well as by 31P NMR spectroscopy. Additionally, their binding properties to complementary oligodeoxynucleotides has been studied.

Chemical nucleic acid synthesis, modification and labelling

The chemical synthesis of RNA on solid phase has now become routine using labile protecting groups and mild deprotection methods. The great interest in antisense technology has sparked the development of P-chiral phosphorothioates and a large number of DNA analogues with modified sugars and/or backbones to increase resistance to nucleases, and with modifier groups attached to the sugar, nucleobase or internucleotide function to aid cellular uptake.