Electrostatic Potential Surfaces for the Cyclobutane Uracil Dimer and Its Radical Ions: Insights into Binding and Catalysis


Olaf Wiest*[2] and Artemio J. Largoza

Department of Chemistry and Biochemistry

University of Notre Dame, Notre Dame IN 46556 (USA)


Received 28 February 1997
Accepted 3 March 1997
Publication date 3 March 1997

Copyright 1997 Internet Journal of Science - Biological Chemistry


The geometries and potential surfaces for the neutral cyclobutane uracil dimer as well as its radical ions have been calculated by ab initio methods. The electronic structure of these species is analyzed using electrostatic potential and spin density surfaces as well as the topology of the frontier molecular orbitals. The overall shape and charge distribution of the cyclobutane uracil dimer suggest a binding mode in which the electrostatic potential pattern in the dimer is matched with the asymmetric distribution of polar and nonpolar amino acid residues in the putative active site of DNA photolyase. The polar interactions between the dimer and the positively charged region of the active site could be enhanced for the radical anion. For the radical cation and the radical anion, a planar cyclobutane ring is calculated. The charges and spin densities are localized at the N1-C6 and C4-C5 positions, respectively. In the radical cation, the C6-C6' bond is substantially stretched and the charge and spin distribution between the rings is almost symmetrical. For the radical anion, a localized structure with an intact C5-C5' bond is obtained.

Table of Contents:

1. Introduction

2. Computational Methodology

3. Results and Discussion

3.1. The cis, syn Cyclobutane Uracil Dimer

3.2. The cis, syn Cyclobutane Uracil Dimer Radical Cation

3.3. The cis, syn Cyclobutane Uracil Dimer Radical Anion

4. Conclusions

5. Acknowledgments

6. References and Footnotes