Polynucleotides. LXIII. Solution conformation of oligodeoxyribonucleotides containing an alternating dC-dG sequence which can form a left-handed double helix

To elucidate the conformational properties and their chain length dependency in solution of oligodeoxyribonucleotides containing an alternating C-G sequence, which have been shown to take a left-handed duplex structure in crystals, d (C-G), d (C-G-C-G) and d (C-G-C-G-C-G) were synthesized by a modified triester method and characterized by ultraviolet (UV) circular dichroism (CD) and 1H-nuclear magnetic resonance (NMR) spectroscopy. The effects of salt concentration (0.1 M and 4 M NaCl), oligomer strand concentration (10-5-10-2M) and temperature (0°-90°C) on the oligomer conformation were investigated. The dimer does not form a duplex under any conditions studied. The tetramer does form a right-handed duplex in 0.1M NaCl even at 3×10-5M strand concentration. In 4M NaCl, however, it does not form any duplex at the same strand concentration, and left-handed duplex formation is observed at 10-fold higher concentration. The hexamer forms a duplex in either salt concentration even at 2×10-5M strand concentration. The melting temperatures of these duplexes were measured by UV and CD methods. The CD-temperature profile in 4M NaCl, which is not sigmoidal when monitored at the λmin of the characteristic negative band, suggests that melting of the high salt duplex is a rather complex process that involves more than two species. The results of 1H-NMR-temperature studies support left-handed duplex formation in a high salt solution.