Synthesis and biophysical evaluation of C-5-triazolyl-functionalized morpholino-thymidine analogs

The C-5 position of pyrimidines has long been a known modification site for fine-tuning the biophysical properties of oligonucleotides and nucleic acid duplexes. In this study, we synthesized a series of C-5-triazole-substituted derivatives of morpholino-uridine nucleosides starting from C-5-ethynyl-morpholino-uridine nucleosides by a copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. These modified monomers were successfully incorporated in a 9-mer PMO sequence using solid-phase synthesis to study their duplex stabilization ability with complementary DNA and RNA strands. A melting temperature study revealed that the 1-phenyltriazol 4-yl moiety stacks more effectively with complementary RNA compared to other derivatives. Furthermore, single incorporations of these monomers generally destabilize PMO : DNA and PMO : RNA duplexes, while three consecutive incorporations invoke thermo-stabilizing effects. These modified PMOs also showed fine to excellent mismatch base discrimination with complementary RNA. The global geometries of the PMO : RNA duplexes were analysed by CD spectroscopy, which confirmed that they adopted somewhere between standard A- and B-type geometries.