Synthesis and properties of oligonucleotides with iodo-substituted aromatic aglycons: investigation of possible halogen bonding base pairs |
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Authors: | Tawarada Ryuya Seio Kohji Sekine Mitsuo |
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Institution: | Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan. |
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Abstract: | Ab initio calculations of halogen bond energies of artificial base pairs constructed between iodinated aromatic nucleobase mimics and nitrogen-containing acceptor molecules such as pyridine and imidazole suggest that modified base pairs are converted to optimized planar base pairs with weak Delta E values of -0.19 to -3.93 kcal/mol. To evaluate the contribution of halogen bonding toward duplex stabilization of such modified nucleobase mimics introduced into artificial base pairs, we synthesized three C-nucleoside analogues 1-3 with several iodinated aromatic rings and an imidazole nucleoside derivative 4 and incorporated them into oligodeoxynucleotides. Hybridization studies of modified oligodeoxynucleotides incorporating iodoaromatic bases showed their unique universal base-like ability; however, no indication of halogen bond formation was observed. A more sophisticated design is required for the development of new base pairs stabilized by halogen bonding. |
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