Publication: Quantum mechanical description of the interactions between DNA and water

Abstract: In recent years, a lot of attention has been focused on the electronic properties of DNA. With recent advances in linear scaling quantum mechanics there are now new tools available to enhance our understanding of the electronic properties of DNA among other biomolecules. Using both explicit solvent models and implicit (continuum) solvent models, the electronic characteristics of a dodecamer duplex DNA have been fully studied using both divide and conquer (D&C), semi-empirical quantum mechanics and non-D&C semi-empirical quantum mechanics. According to the AM1 Hamiltonian, 3.5 electrons (0.3 electron/base pair) are transferred from the duplex to the solvent. According to the density of state (DOS) analysis, in vacuo DNA has a band gap of 1 eV showing that in the absence of solvent, the DNA may exhibit similar properties to those of a semiconductor. Upon increasing solvation (2.5–5.5 Ã…), the band gap ranges from 3 eV to 6 eV. For the implicit solvent model, the band gap continues this widening trend to 7 eV. Therefore, upon solvation and in the absence of dopants, the DNA should begin to loose its conductive properties. Finally, when one considers the energy and localization of the frontier orbitals (HOMO and LUMO), solvent has a stabilizing effect on the DNA system. The energy of the HOMO drops from 15 eV in vacuo to 2 eV for 5.5 Ã… of water to −8 eV for the implicit solvent model. Similarly, the LUMO drops from 16 eV for in vacuo to 9 eV for 5.5 Ã… of water to −1 eV for the implicit model. Beyond the importance of the computed results on the materials properties of DNA, the present work also shows that the behavior of intercalators will be affected by the electronic properties of DNA. This could have an impact on our understanding of how DNA based drugs interact with DNA and on the design of new DNA based small molecule drugs.

Authors: Lance M. Westerhoff and Kenneth M. Merz, Jr.

Reference: J. Mol. Graph. Mod. 2006, 24(6), 440-455. (see link for full paper).