Phosphoramidite derivatives

Many other catalysts and ligands have been examined for the enantioselective reduction of a-acetamidoacrylates and related substrates. Phosphoramidites derived from BINOL and the cyclic amines piperidine and morpholine give excellent results.35... 

The conjugation of oligonucleotides with peptides also can be done using Diels-Alder cycloadditions in water (Tona and Haner, 2005). Marchan et al. (2006) used the same 3,5-hexadiene phosphoramidite derivative as Hill et al. (2001), but in this case used a maleimide-modified... 

Protection and activation of the phosphate moiety is achieved by employing a phosphoramidite derivative, -P(OR)NR2. This reagent has phosphorus in its P " oxidation state the phosphate that we finally require contains P. Favoured R groups in the... 

The dimethoxytrityl ester protecting group is now removed by treatment with mild acid (CCI3CO2H), which is insufficiently reactive to hydrolyse the amide protection of bases, or the cyanoethyl protection of the phosphate. The coupling cycle can now be repeated using a phosphoramidite derivative of the next appropriate nucleoside. The sequences will be continued as necessary until the desired oligonucleotide is obtained. 

Several fluorescent labeling dyes are commercially available (Alexa series, Oregon green, Rhodamine and Cyanine dyes, etc.). They are all characterized by the presence of double bonds on every other carbon atom of a cyclic structure, containing the electron that once on excitation emitted fluorescent light. The cyanine dyes are the most widely used at the moment. They are bright, easily added to the nucleotides, stable to photo-bleaching and with a Stokes shift value of about 20 nm. The cyanine dyes used in microarray analysis are Cy3 (absorption at 550 nm and emission at 570 nm) and Cy5 (absorption at 649 nm and emission at 670 nm) that are already available as phosphoramidite derivatives. 

The unprotected 5-hydroxy group is then reacted with a 3-phosphoramidite derivative of the next nucleoside in the presence of tetrazole, which acts as a weak acid catalyst. (These phosphoramidite derivatives are now commercially available.) The diisopropylamino group is displaced by the 5-hydroxy group, and the phosphorus-oxygen bond is formed. 

The phosphoramidite derivative of N-nitrothymidine (44) has been synthesised and found suitable for oligonucleotide synthesis using a standard phosphite triester solid phase approach. The N-nitrothymidine residues could be converted into a range of N -modified thymidines by reaction with primary alkyl amines. Phosphoramidite derivatives of 4-nitroindazole N and N -(2 -deoxy-p-D-ribofuranosides) (45, 46) have been synthesised, their base pairing properties investigated and found to show ambiguous base pairing. Seela has also reported the syntheses of the phosphoramidite derivatives of 8-aza-7-adenine... 

Another type of convertible nucleoside phosphoramidite, a derivative of (5 S)-5 -C-(5-bromo-2-penten-l-yl)-2 -deoxyribosylfuranosyl thymidine (49), has been reported. The synthesis of this phosphoramidite was stereoselective and involved a Sakurai reaction between 5 -C-thymidine aldehyde and allyltrimethylsilane. Seela has reported the synthesis of the ribosyl-phosphoramidite derivatives of 7-bromo- and 7-iodo-8-aza-7-deazapurine-2,6-diamine (50a,b) from advanced synthetic precursors and of the bromo- and iodo-derivatives at the 5-position of uracyl phosphoramidite (51a,b). He further described the effect on base-pair stability due to their incorporation into oligonucleotide duplexes. ... 

There are also a number of new dye-modified analogues for use in FRET analysis. A new four colour set of FRET dideoxy 5 -triphosphate terminators has been developed involving a rigid, linear ET cassette linker chemistry, and formulated with Thermo Sequenase II DNA polymerase. An alternative approach for a four colour set of FRET dyes has been reported where the dyes are incorporated into ODNs as phosphoramidite derivatives. ... 

Benhida described the synthesis of a 2-deoxy-C-nucleoside analogue and its phosphoramidite derivative featuring 6-(thiazolyl-5)-a-benzimidazole nucleobase (134). A more efficient route to the expanded adenosine analogue (135) was developed by Kool, who also described the synthesis of the expanded thymidine analogue (136) starting from 5-methylanthranilic acid. Both nucleosides were found to be efficient fluorophores. 3 -Cyanoethyl phosphoramidites of 6-methyl-3-(2 -deoxy-(3-D-ribofuranosyl)-3//-pyrrolo[2,3-d]pyrimidin-2-one... 

A selective method which involves the selective pivaloyloxymethyl protection of the N1 of pseudouridine followed by methylation at N3 was developed to prepare the 5-benzhydryloxybis(trimethylsilyloxy)silyl, bis(2-acetoxy-ethoxy)me-thyl- protected phosphoramidite derivative (139) of the nucleoside 3-methylpseu-douridine. The methylated pseudouridine phosphoramidite was successfully used in oligonucleotide synthesis for the NMR study of helix 69 of E. coli 23S rRNA. 2-Thiouridines incorporating 2 -modified nucleoside phosphoramidites... 

Kool described the synthesis of the phosphoramidite derivative of a C-nucleoside incorporating a porphyrin moiety, (146)." His approach was to assemble the porphyrin de novo on the sugar moiety starting from 3,5-bis-O-toluoyl-protected deoxyribose-Cl-carboxaldehyde, benzaldehyde and dip-yrromethane under Lindsey conditions. Similarly, to fluorescently label oligonucleotides, Burgess reported the synthesis of phosphoramidite (147), for which the nucleoside precursor was prepared from 5-ethynyl thymidine and iodofluorescein via Sonogashira s coupling procedure. ... 

A series of analogues of the decamer d(GGGAATTCCC) have been prepared in which the nucleosides are sequentially replaced by (t)-butan-l,3-diol to give oligodeoxyrlbonucleotides that lack the deoxyrlbose moiety at the chosen position. The diol unit was converted into the phosphoramidite derivative... 

---