Phosphoramidite cycle

In step 1 of each oligonucleotide-synthesis cycle the 5 -terminal 4,4 -dimethoxytrityl protecting group is removed with trichloroacetic acid, and the support is washed with acetonitrile to prevent dctritylation of the next incoming phosphoramidite. The 4,4 -dimethoxy-... 

Concurrent with studies on cyclometalation, studies on the effects of the structure of phosphoramidite ligand had been conducted. Several groups studied the effect of the stmcmre of ligand on the rate and selectivity of these iridium-catalyzed allylic substitutions. LI contains three separate chiral components - the two phenethyl moieties on the amine as well as the axially chiral BINOL backbone. These portions of the catalyst structure can control reaction rates by affecting the rate of cyclometalation, by inhibiting catalyst decomposition, or by forming a complex that reacts faster in the mmover-limiting step(s) of the catalytic cycle. 

Scheme 22 Catalytic cycle for the reaction of aniline with methyl cinnamyl carbonate catalyzed by a metalacyclic iridium-phosphoramidite complex...

Scheme 9.10 Catalytic cycle of the allylic substitution catalyzed by (phosphoramidite)It complexes.

Fig. 19 Basic steps in a cycle of nucleotide addition by the phosphoramidite method in-situ synthesis using ink-jetting. DMTr = dimethoxytrityl group...

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. 

A last possibility to obtain probes grafted onto beads is to directly synthesize the oligonucleotide probes onto glass beads via phosphoramidite reaction [18] (Fig. 6). The synthesis reaction sequence is composed of a coupling step between a protected nucleotide immobilized onto the bead and a tetra-zole activated and protected nucleotide (step C). This is followed by a capping and a de-blocking of the newly added nucleotide (step D and B). The cycle is then repeated until the desired sequence is obtained. 

Fig. 6 Schematic representation of the phosphoramidite nucleic acid sequence synthesis onto glass beads de-blocking (a), (b), base condensation (c), capping and oxidation (d) are illustrated. This cycle is completed once for each additional base desired...

Figure 5-22. Oligodeoxynudeotide synthesis by any unreacted OH groups are blocked in a cap-the phophoramidite method. The free OH group ping step. The protecting dimethoxytrityl group of the previous nucleotide building block reacts is removed in preparation for a new cycle of with the incoming phosphoramidite. After oxida- reaction, tion to the protected phosphotriester,...

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