Still Elusive - Pd(II)-Mediated Base Pairing by an Acetophenone Oxime Palladacycle within 15N-Labelled Double-Helical Oligonucleotides

Both alpha and beta anomers of an acetophenone C-nucleoside were synthesized and incorporated in the middle of short oligodeoxynucleotides. The ketone oligonucleotides were converted to N-15-labelled oxime oligonucleotides by treatment with N-15-hydroxylamine and, finally, cyclopalladated by treatment with lithium tetrachloropalladate. Comparison of the UV melting profiles of duplexes bearing the beta anomer of either the palladacyclic or the metal-free oxime C-nucleoside suggested formation of a stable Pd(II)-mediated base pair, especially with adenine or thymine as the base pairing partner. Melting profiles of the corresponding duplexes bearing the alpha anomer were much more convoluted, precluding meaningful comparison. N-15 NMR spectra were obtained for the beta anomeric oxime oligonucleotide as well as its palladacyclic derivative but the signals unfortunately diminished below detection limit when the latter was hybridized with a complementary strand placing a (15)N3-labelled thymine opposite to the palladacyclic residue.

Automated summary

Both alpha and beta anomers of an acetophenone C-nucleoside were synthesized and incorporated in the middle of short oligodeoxynucleotides. The ketone oligonucleotides were converted to N-15-labelled oxime oligonucleotides and cyclopalladated. Comparison of the UV melting profiles suggested formation of a stable Pd(II)-mediated base pair with adenine or thymine as the base pairing partner. The N-15 NMR spectra indicated successful labeling, but the signals diminished below detection limit when hybridized with a complementary strand in a specific configuration.