Synthesis and activity of modified cytidine 5'-monophosphate probes for T4 RNA ligase 1

We describe the synthesis of a series of unique base modified ligation probes such as p(5')C-4-ethylenediamino 3, p(5')C-4-biotin 4, and pre-adenylated form A(5')pp(5')C-4-biotin 6 and tested their biological activity with T4 RNA ligase 1 using a standard pCp probe 1 as a control. The intermolecular ligation assay was developed using a 5'-FAM labeled 24 mer single-stranded (ss) RNA and the average ligation efficiencies for pCp 1, p(5')C-4-ethylenediamino 3, p(5')C-4-biotin 4, and pre-adenylated form A(5')pp(5')C-4-biotin 6 were found to be 44%, 81%, 39% and 16% respectively, as determined using a denaturing gel analysis. Furthermore, confirmation of the ligation activity of the biotinylated probes to the RNA substrate was confirmed by streptavidin conjugation and analysis by nondenaturing gel electrophoresis. These results strongly suggest that the new probes are valid substrates for T4 RNA ligase 1 and therefore could be useful for developing a miRNA detection system that includes rapid isolation, efficient labeling and detection of miRNAs on sensitivity-enhanced microarrays.