Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data

Abstract

We have derived a complete set of atomic charges for DNA from very high resolution, low temperature, single-crystal X-ray diffraction data, collected for a variety of nucleosides and nucleotides: cytidine; deoxycytidine 5'-monophosphate; deoxythymidine; guanosine 5'-monophosphate; deoxyadenosine; adenosine. This set of charges represents the first experimentally based parameterization of an important term in the energy function used in most modeling of DNA. The resulting charges are in good agreement with chemical intuition and experimental observations. They also agree qualitatively with the theoretically derived values now commonly used, but numerous and significant quantitative differences are observed. Possible reasons for the quantitative disagreement are discussed. An averaged set of charges (derived from the experimental results), which can be used in DNA modeling calculations, is presented.