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Nucleic Acids Symposium Series 2003 3(1):49-50; doi:10.1093/nass/3.1.49
© 2003 by Oxford University Press
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Important factors stabilizing stacking interaction between 3-nitropyrrole and natural nucleobases revealed by ab initio calculations

Kohji Seio1,3, Hisashi Ukawa2, Koh-ichiro Shohda2 and Mitsuo Sekine2,3

1 Frontier Collaborative Research Institute, Tokyo Institute of Technology, Nagatsuta Midori-ku, Yokohama 226-8501, Japan, 2 Department of Life Science, Tokyo Institute of Technology, Nagatsuta Midori-ku, Yokohama 226-8501, Japan, 3 CREST, JST (Japan Science and Technology Corporation), Nagatsuta Midori-ku, Yokohama 226-8501, Japan

Stacking energies between canonical nucleobases and a universal base, 3-nitropyrrole (3-NP), were estimated by use of molecular orbital (MO) and molecular mechanics (MM) calculations. The detailed analysis of the energy profiles revealed the importance of the London dispersion energy to stabilize the stacked dimers and electrostatic interactions to determine the orientation of 3-NP to the nucleobases in the dimers.

Although the energy profiles of 3-NP/natural base dimers obtained by the MO and MM calculations were qualitatively correlated with each other, the correlations were poorer than those obtained for the stacking between natural bases. The origin of the difference between 3-NP and natural bases will be discussed to understand the possibility and limitation of the current MM calculations for the simulation and design of other universal bases.


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