Synthesis and properties of uniquely modified oligoribonucleotides: Yeast tRNA(Phe) fragments with 6-methyluridine and 5,6-dimethyluridine at site-specific positions

The phosphoramidites of 6-methyluridine and 5,6-dimethyluridine were synthe sized and the modified uridines site-selectively incorporated into heptadec amers corresponding in sequence to the yeast tRNA(Phe) anticodon and T Psi C domains. The oligoribonucleotides were characterized by NMR, MALDI-TOF MS and UV-monitored thermal denaturations. The 6-methylated uridines retained the syn conformation at the polymer level and in each sequence location de stabilized the RNAs compared to that of the unmodified RNA. The decrease in RNA duplex stability is predictable. However, loss of stability when the m odified uridine is in a loop is sequence context dependent, and can not, at this time, be predicted from the location in the loop.