NMR-STUDIES OF G-A MISMATCHES IN OLIGODEOXYRIBONUCLEOTIDE DUPLEXES MODELED AFTER RIBOZYMES

The structures of two oligodeoxyribonucleotide duplexes, the base sequ ences of which were modelled after both a hammerhead ribozyme and a sm all metalloribozyme, were studied by NMR. Both duplexes contain adjace nt G:A mismatches; one has a PyGAPu:PyGAPu sequence and the other a Py GAPy:PuGAPu sequence. It is concluded on the basis of many characteris tic NOEs that in both duplexes G:A base pairs are formed in the unique 'sheared' form, where an amino proton instead of an imino proton of G is involved in the hydrogen bonding, and G and A bases are arranged ' side by side' instead of 'head to head'. A photo-CIDNP experiment, whi ch gives unique and independent information on the solvent accessibili ty of nucleotide bases, also supports G:A base pairing rather than a b ulged-out structure of G and A residues. This is the first demonstrati on that not only the PyGAPu:PyGAPu sequence but also the PyGAPy:PuGAPu sequence can form the unique sheared G:A base pairs. Taking the previ ous studies on G:A mismatches into account, the idea is suggested that a PyGA:GAPu sequence is a minimum and essential element for the forma tion of the sheared G:A base pairs. The sheared G:A base pairs in the PyGAPu:PyGAPu sequence are suggested to be more stable than those in t he PyGAPy:PuGAPu sequence. This is explained rationally by the idea pr oposed above.