Influence of the type of junction in DNA-3 '-peptide nucleic acid (PNA) chimeras on their binding affinity to DNA and RNA

The automated on-line synthesis of DNA-3'-PNA (PNA = Polyamide Nucleic Acid s) chimeras 1-3 is described, in which the 3'-terminal part of the oligonuc leotide is linked to the aminoterminal part of the PNA either via a N-(2-me rcaptoethyl)- (X = S), a N-(2-hydroxyethyl)- (X = O), or a N-(2-aminoethyl) - (X = NH) N-[(thymin-1-yl)acetyl]glycine unit. Furthermore, the DNA-3'-PNA chimera 4 without a nucleobase at the linking unit was prepared. The bindi ng affinities of all chimeras were directly compared by determining their T -m values in the duplex with complementary DNA, RNA, or DNA containing a mi smatch or abasic site opposite to the linker unit. We found that all invest igated chimeras with a nucleobase at the junction form more stable duplexes with complementary DNA and RNA than the corresponding unmodified DNA. The influence of X on duplex stabilization was determined to be in the order O > S approximate to NH, rendering the phosphodiester bridge the most favored linkage at the DNA/PNA junction. The observed strong duplex-destabilizing effects, when base mismatches or non-basic sites were introduced opposite t o the nucleobase at the DNA/PNA junction, suggest that the base at the link ing unit contributes significantly to duplex stabilization.