Condensing agents, oligonucleotide synthesi

A further unusual feature of the matrix-dependent polycondensation lies in the character of the nucleobases themselves. Purine mononucleotides undergo polycondensation, in good yields, at complementary matrices consisting of pyrimidine polymers. However, the synthesis of pyrimidine oligonucleotides from their mononucleotides at purine matrices is not effective. This important fact means that a pyrimidine-rich matrix leads to a purine-rich nucleic acid, which is itself not suitable to act as a matrix. This phenomenon also occurs when matrices are used which contain both basic species, i.e., purines and pyrimidines. An increase in the amount of purine in a matrix leads to a clear decrease in its effectiveness (Inoue and Orgel, 1983). However, the authors note self-critically that the condensation agent used cannot be considered to be prebiotic in nature. 

Reese CB, Ubasawa A. Namre of side-reactions in oligonucleotide synthesis involving arenesulphonyl derivatives of 3-nitro-1,2,4-triazole and related condensing agents. Nucleic Acids Symp. Ser. 1980 (7) 5-21. 

Trichloroethanol has been used as a protecting group in the triester approach for the synthesis of deoxyribo- [29] as well as ribo-oligonucleotides [30]. It can be removed selectively by reduction with Zn or Zn/Cu, as previously discussed. The triesters may be synthesized either by stepwise addition of the two properly protected nucleosides to, , -trichloroethyl phos-phorodichloridate (Fig. 6.11a) or by condensation of a/3, 3, 3-tri-chloroethyl ester of a nucleotide with a nucleoside using an arylsulphonyl chloride as a condensing agent (Fig. 6.11b). 

Condensation Reagent. As a reagent l//-tetrazole has been used as a condensation agent to mediate the coupling of ribonucleotides and phosphoramidites in the synthesis of oligonucleotides. l//-tetrazole has also been used to promote the coupling of phosphoramidite and protected inositols for the synthesis of myo-inositol phosphates (eq 11). ... 

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