Peptide nucleic acids (PNA) derived from N-(N-methylaminoethyl)glycine. Synthesis, hybridization and structural properties

Backbone N-methylated peptide nucleic acids (PNAs) containing the four nucl eobases adenine, cytosine, guanine and thymine were synthesized via solid p hase peptide oligomerization. The oligomers bind to their complementary tar get with a thermal stability that is 1.5-4.5 degrees C lower per "N-methyl nucleobase unit" [dependent on the number and position(s) of the N-methyl] than that of unmodified PNA. However, even fully N-methyl modified PNAs bin d as efficiently to DNA or RNA targets as DNA itself. Furthermore, the hybr idization efficiency per N-methyl unit in a PNA decreased with increasing N -methyl content, and the effect was more pronounced when the N-methyl backb one units are present in the Hoogsteen versus the Watson-Crick strand in (P NA)(2)-DNA triplexes. Interestingly, CD spectral analyses indicate that 30% (3 out of ten) substitution with N-methyl nucleobases did not alter the st ructure of PNA-DNA (or RNA) duplexes or (PNA)(2)-DNA triplexes, and likewis e CD spectroscopy and X-ray crystallography showed no major structural diff erences between N-methylated (30%) and unmodified PNA-PNA duplexes. However , PNA-DNA duplexes as well as triplexes adopted a different conformation wh en formed with all-Ai-methyl PNAs.