Synthesis and properties of oligonucleotides with iodo-substituted aromatic aglycons: investigation of possible halogen bonding base pairs.
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.
Tawarada
Ryuya
R
Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan.
Seio
Kohji
K
Sekine
Mitsuo
M
D020029:Base Pairing; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D006847:Hydrocarbons, Iodinated / Q000737:chemistry*; D008956:Models, Chemical; D015394:Molecular Structure; D009705:Nucleosides / Q000138:chemical synthesis / Q000737:chemistry*; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000737:chemistry; D011789:Quantum Theory
D006847:Hydrocarbons, Iodinated; D009705:Nucleosides; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D004247:DNA