Synthesis and Evaluation of MGB Polyamide-Oligonucleotide Conjugates as Gene Expression Control Compounds

MGB polyamide-oligonucleotide conjugates ON 1-4 with linked MGB polyamides at the 2-exocyclic amino group of a guanine base using aminoalkyl linkers were synthesized and evaluated in terms of binding affinity for complementary DNA containing the MGB polyamide binding sequence using T-m and CD analyses. The MGB polyamides comprised pyrrole polyamides (Py-4- and Py-3-), which possess binding affinity for A-T base pairs, and imidazole (Im(3)-) and pyrrole-?-imidazole (Py-3-?-Im(3)-) polyamide hairpin motifs, which possess binding affinity for C-G base pairs. It was found that the stability of modified dsDNA was greatly influenced by the linker length. Py-4- and Py-3-oligonucleotide conjugates (ON 1 (n=4) and ON 2 (n=4)) containing the 4-aminobutyl linker formed stable dsDNA with complementary DNA. Although Im(3)-oligonucleotide conjugate ON 3 (n=4) containing the 4-aminobutyl linker formed stable dsDNA with complementary DNA, stabilization of dsDNA by the imidazole amide moiety of ON 3 (n=4) was lower compared with the pyrrole amide moiety of ON 2 (n=4). The Py-3-?-Im(3)-oligonucleotide conjugate ON 4 (n=2), which possesses binding affinity for C-G base pairs via a pyrrole/imidazole combination and contains a 2-aminoethyl linker, showed high binding ability for complementary DNA. Furthermore, the DNA sequence recognition of MGB polyamide-oligonucleotide conjugates was investigated using single-base mismatch DNAs, which possess a mismatch base in the MGB polyamide binding sequence. The Py-3-?-Im(3)-oligonucleotide conjugate ON 4 (n=2) showed high sequence recognition ability for complementary DNA.