Comparison of substrate base sequences for RNA ligase reactions in the synthesis of a tetradecanucleotide corresponding to bases 21-34 of E. coli tRNAfMet 1.

A tetradecanucleotide U-A-G-C(U-C-G)2G-G-C-Up corresponding to bases 21-34 of a nascent sequence of formylmethionyl tRNA of E. coli has been synthesized by the joining of two combinations of chemically synthesized oligonucleotides: 1) U-A-G-C + U-C-G-U-C-G + G-G-C-Up and 2) U-A-G-C + U-C-G-U + C-G-G-G-C-Up. In reaction 1) and the extent of joining *pG-G-C-Up to U-C-G-U-C-G was only 15.4% and the last ligation of the decamer to U-A-G-U proceeded to 27%. In reaction 2) joining between U-A-G-C and pU-C-G-Up gave a high yield (88%). The ligation of this octamer and *pC-G-G-G-C-Up also gave a satisfactory yield (52%). These reactions suggest that sequence preferences in RNA ligase reactions may arise from the structure of the 3'-end of acceptor molecules.