Oligonucleotides protecting groups

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-... 

The protected nucleoside-3-phosphoramidite monomer units such as 671 are used in the solid-phase oligonucleotide synthesis. In the 60mer synthesis, 104 allylic protective groups are removed in almost 100% overall yield by the single Pd-catalyze reaction with formic acid and BuNH2[432], N,(9-protection of uridine derivatives was carried out under pha.se-transfer conditions[433]. 

A number of standard synthetic reference books are available. A review article by Kossell and Seliger discusses protective groups used in oligonucleotide syntheses, including protection for the phosphate group, which is not included in this book, and a series of articles describe various aspects of protective group chemistry. 

This substantial group was developed as a fluorescent, acid-labile protective group for oligonucleotide synthesis. It has properties very similar to those of the DMTr group except that it can be detected down to 10 M on TLC plates with 360-nm ultraviolet light. 

The Dnseoc group was developed as a base-labile protective group for the 5 -hydroxyl in oligonucleotide synthesis. It is cleaved with DBU in aprotic solvents. The condensation of oligonucleotide synthesis can be monitored by UV detection at 350 nm or by fluorescence at 530 nm of the liberated vinylsulfone. ... 

The steps involved in automated oligonucleotide synthesis illustrate the current use of protective groups in phosphate chemistry (Scheme 1). Oligonucleotide synthesis involves the protection and deprotection of the 5 -OH, the amino groups on adenine, guanine, and cytosine, and -OH groups on phosphorus. 

The disadvantage of this method is that the dichloridites and monochloridites are sensitive to water and thus could not be used readily in automated oligonucleotide synthesis. This problem was overcome by Beaucage and Caruthers, who developed the phosphoramidite approach. In this method, derivatives of the form R 0P(NR2)2 react with one equivalent of an alcohol (catalyzed by species such as l//-tetrazole) to form diesters, R OP(OR")NR2, which usually are stable, easily handled solids. These phosphoroamidites are easily converted to phosphite triesters by reaction with a second alcohol (catalyzed by l//-tetrazole). Here, again, oxidation of the phosphite triester with aqueous iodine affords the phosphate triester. Over the years, numerous protective groups and amines have been examined for use in this approach. Much of the work has been reviewed. ... 

The trifluoroethyl group was used as an activating group in the phosphotriester approach to oligonucleotide synthesis, as well as a protective group that could be removed with 4-nitrobenzaldoxime (tetramethylguanidine, dioxane, H20). ... 

The lipophilicity of this phosphate protective group helps in the chromatographic purification of oligonucleotides. It is removed by the oximate method. ... 

The rate of oligonucleotide synthesis by the triester method using mesitylenesul-fonyl chloride was increased five- to tenfold when this group was used as a protective group during intemucleotide bond formation. It was removed with coned. NH4OH at 60° for 12 h or by the oximate method. ... 

This highly lipophilic group is cleaved with isoamyl nitrite in Pyr/AcOH. The use of a lipophilic 5 -phosphate protective group aids in reverse-phase HPLC purification of oligonucleotides. 

As mentioned in last year s Report, aromatic phosphoramidates have been used to protect 5 -phosphoryl groups in the stepwise synthesis of oligodeoxyribonucleotides. The appropriate monomer units are coupled with DCC and the phosphoramidate protecting group is removed when required with isoamyl nitrite. A rapid and general preparative method for oligonucleotides has been developed based on phosphoramidates of the highly lipophilic 4-aminophenyltriphenylmethane (25). Purification of... 

Although use of automated oligonucleotide synthesis is widespread, work continues on the optimization of protecting groups, coupling conditions, and deprotection methods, as well as on the automated devices.56... 

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. 

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