Oligoribonucleotide synthesis deprotection

Wincott F, DiRenzo A, Shaffer C, Grimm S, Tracz D, Workman C, Sweedler D, Gonzalez C, Scaringe S, Usman N. Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res 23 2677-2684, 1995. Sproat B, Coloima F, Mullah B, Tsou D, Andrus A, Hampel A, Vinayak R. An efficient method for the isolation and purification of oligoribonucleotides. Nucleosides Nucleotides 14 255-273, 1995. 

Currently, the 5 -DMT/2 -TBDMS combination constitutes the benchmark for the synthesis of oligoribonucleotides. Although many other methods for the synthesis of RNA have been developed, none have gained the popularity of the TBDMS chemistry. Advances in the use of this silyl chemistry in both synthesis [7,8] and deprotection [7,8,61] strategies have made it an even more viable approach to the production of oligoribonucleotides. 

Figure 10 HPLC chromatograms of a 36-mer oligoribonucleotide (5 -GUU UUC ecu GAU GAG GCC GAA AGG CCG AAA UUC UCC-3 ) synthesized at the 0.2- tmol scale according to the basic synthesis protocol and deprotected using the second alternative one-pot deprotection protocol. A, 0.25 M SET B, 0.5 M DCI C, 0.45 M TET. Dionex NucleoPac PA-100 22 X 250 mm colunm at 50°C. Buffer A (1 mM Tris, 20 mM NaC104), buffer B (1 mM Tris, 300 mM NaC104). Gradient 40% B to 70% B in 12 min, flow rate, 1.5 mL/min.

At a small scale (<10 fjmoV), the quality of oligoribonucleotides generated from the basic and alternative deprotection protocols does not vary much. Therefore, one should consider the timing requirement as an important parameter in selecting a particular protocol. However, because oligori-bonucleotide synthesis often incorporates one or more modified synthons that may be more or less sensitive to the basic or fluoride treatments, the chemical compatibility should be examined carefully before selecting the optimal deprotection method. 

Reddy MP, Hanna NB, Farooqui F. Methylamine deprotection provides increased yield of oligoribonucleotides. Tetrahedron Lett 36 8929-8932, 1995. Reddy MP, Farooqui F, Hanna NB. Elimination of transamination side product by the use of dCAc methylphosphonamidite in the synthesis of oligonucleo-side phosphoramidites. Tetrahedron Lett 37 8691-8694, 1996. 

---