Stabilization of G•C-Containing DNA Duplexes by Polyamides with Parallel Orientation in the Minor Groove

The polyamides based on 4-amino-1-methylpyrrol-2-carboxylic acid, 4-amino-1-methylimidazole-2-carboxylic acid, and β-alanine that stabilize oligonucleotide duplexes consisting of G•C pairs through parallel packing in the minor groove were studied. The initial duplex TTGCGCp•GCGCAA melts at 28°C; the TTGCGCp[NH(CH2)3COPyImβImNH(CH2)3NH(CH3)2][NH(CH2)3COImβImPyNH(CH2)3N(CH3)2]•GCGCAA duplex (bisphosphoramidate with parallel orientation of ligands, where Py, Im, and β are the residues of 1-methyl-4-aminopyrrol-2-carboxylic and 1-methyl-4-aminoimidazole-2-carboxylic acids and β-alanine, respectively), at 48°C; and the TTGCGCp[NH(CH2)3COImβImPyNH(CH2)3COImβImPyNH(CH2)3N(CH3)2]•GCGCAA duplex (a hairpin structure with antiparallel orientation), at 56°C.