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Artificial base pairs by use of halogen bonding were designed and their interaction energies were estimated by ab initio calculations. The optimized structures of the artificial base pairs were almost consistent with those of the canonical base pairs, and the interaction energies were ca. 5-11 kcal/mol. To investigate the thermal stability of the base pairs containing halogen bonds in oligodeoxynucleotide duplexes, deoxynucleoside 3'-phosphoramidite building blocks as halogen bonding acceptors and donors were synthesized and used for incorporation into oligodeoxynucleotides. UV-melting experiments suggest that these halogen bonding base pairs have low stability compared with the A-T base pair. Furthermore, the effect of the halogen bonding on stabilization of duplexes was studied in detail by comparison with the hybridization ability of oligodeoxynucleotides containing a modified base having a iodo group with that of the complementary DNA strands lacking the donor site.

Synthesis and properties of artificial base pairs by use of halogen bonds