Synthesis and Biophysical Studies of High-Affinity Morpholino Oligomers Containing G-Clamp Analogs

J Org Chem. 2023 Nov 3;88(21):15168-15175. doi: 10.1021/acs.joc.3c01658. Epub 2023 Oct 16.

Abstract

Successful syntheses of chlorophosphoramidate morpholino monomers containing tricyclic cytosine analogs phenoxazine, G-clamp, and G8AE-clamp were accomplished. These modified monomers were incorporated into 12-mer oligonucleotides using trityl-chemistry by an automated synthesizer. The resulting phosphorodiamidate morpholino oligomers, containing a single G-clamp, demonstrated notably higher affinity for complementary RNA and DNA compared to the unmodified oligomers under neutral and acidic conditions. The duplexes of RNA and DNA with G-clamp-modified oligomers adopt a B-type helical conformation, as evidenced by CD-spectra and show excellent base recognition properties. Binding affinities were sequence and position dependent.

MeSH terms

  • DNA* / chemistry
  • Morpholinos / chemistry
  • Nucleic Acid Conformation
  • Oligonucleotides* / chemistry
  • RNA / chemistry

Substances

  • Morpholinos
  • 9-(2-aminoethoxy)phenoxazine
  • Oligonucleotides
  • DNA
  • RNA