Oligonucleotides trityl

Benzyl ethers bearing electron-donating groups can be cleaved by treatment with acids or oxidants. The rate of solvolysis increases with the number of electron-donating groups, and in the series benzyl < benzhydryl < trityl. For the solid-phase synthesis of oligonucleotides, the 5 -hydroxyl group is usually protected as 4,4/-dimethoxytrityl... 

Formation of p-Lactams, Peptides and Oligonucleotides. The intramolecular cyclization technology to form /8-lactams using DCC in the condensation reaction was used by Sheehan and Henery-Logan in the total synthesis of penicilline in 1957. They also found that N-trityl penicilloates are cyclized with diisopropylcarbodiimides. Other p-lactames, such as cephalothin lactone and (—)-thienamicin are similarly constructed. The latter synthesis proceeds in a stereospecific manner and DCC is used in combination with triethylamine to give a 93 % yield of the /3-lactam 661. 

Protective group for nucleosides. Stepwise synthesis of oligonucleotides utilizing 2-cyanoethyl phosphate (1, 172-173) requires protection of the 3 -hydroxyl group which can be cleaved under essentially neutral conditions, since a methoxy-trityl ether is sensitive to acid and a /3-cyanoethyl phosphoric ester is sensitive to alkali. The /3-benzoylpropionyl group meets these requirements, since it is quantitatively cleaved by dilute solutions of hydrazine hydrate in pyridine-acetic acid. The esters are prepared by condensation with DCC (dicyclohexylcarbodiimide). Definitive paper R. L. Letsinger and P. S. Miller, Am. Soc., 91, 3356 (1969)... 

The only exception was an attempt at the 5 -to-3 solid-phase oligonucleotide synthesis using nucleoside 3 -H-phosphonate monoesters, polymer-bound through a trityl-type linker, and oxidative coupling conditions (HgCl2) [123], The H-phosphonates were produced by phosphitylation of the polymer-bound N-unpro-tected nucleoside with phosphorus trichloride followed by hydrolysis by aqueous pyridine [61c]. However, despite some advanced features [124] the stepwise yields were comparable with those in the contemporary phosphodiester method-that is they were too low for the method to be truly competitive. 

Interest in highly cross-linked (20-30% DVB) macroporous polystyrene arose in the early days of oligonucleotide synthesis [158]. It has been argued that this type of support allows for faster reaction kinetics than the low cross-linked gel-type polystyrene. Modified with a trityl-type tinker, it has been tested by Roster and Cramer [159] in the phosphodiester method. The limitations of the chemistry hampered its use for oligomers longer than a few nucleotides. 

The most common trityl anchor was monomethoxytrityl (Figure 19.5), employed in the phosphodiester method on PS-1% DVB by Melby and Strobach [146], on macroporous PS by Roster and Cramer [159] and on PTFE grafted polystyrene by Potapov d. al. [167] A dimethoxytrityl linker was used by Roster and Cramer for the phosphodiester chemistry on popcorn PS [144] and by Belagaje and Brush [155] for their original adaptation of the phosphotriester method for the synthesis in 5 -to-3 direction (Figure 19.5). Roster has also described a trityl anchor linked to a silica gel support [185]. Similar linkers have been exploited for liquid-phase oligonucleotide synthesis (Section 19.4). 

A reagent to attach an amino bearing trityl group, (210), has been reported. After DNA synthesis the amino function was liberated and acylated with N-hydroxysuccinimidyl p-benzoylbenzoate. The resultant oligonucleotide could... 

In a study on the potential of a series of substituted trityl groups in oligonucleotide synthesis, the (p-bromophenacyloxyphenyl)diphenyl-methyl group (28) appeared to have several advantages. On account of its size the chloride derived from (28) reacted only with 5 -hydroxy-groups of nucleosides and could easily be removed by the action of zinc and acetic... 

At the end of the synthesis, perform a manual detritylation cycle, if desired, to remove the trityl group at the 5 -end of the oligonucleotide. 

If oligonucleotide has been synthesized trityl-off, proceed to quench and desalting steps according to steps 8-10 in Section V.D.l. 

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