SYNTHESIS AND HYBRIDIZATION PROPERTIES OF AN ACYCLIC ACHIRAL PHOSPHONATE DNA ANALOG

Protected N-(2-hydroxyethyl)-N-(nucleobase-acetyl) acids (6a-d) of all four DNA nucleobases have been prepared and oligomerized by solid-pha se synthesis. Four DNA decamers containing 1-10 of these 'PPNA' monome rs were prepared and evaluated by T-m measurements (medium salt) for b inding to their DNA and RNA complements. One central modification redu ced the binding strongly (Delta T-m = -10 degrees C), but contiguous P PNA monomers gave smaller effects, and the all-PPNA decamer bound to R NA with a Delta T-m of -1.2 degrees C per modification. Thus PPNA olig omers are inferior DNA and RNA binders compared to the closely related and strongly binding PNA oligomers. (C) 1998 Elsevier Science Ltd. Al l rights reserved.