Calculated state densities of aperiodic nucleotide base stacks

Electronic density of states (DOS) histograms and of the nucleotide base st ack regions of a segment of human oncogene (both single and double stranded , in B conformation) and of single-stranded random DNA base stack (also in B conformation), were calculated. The computations were performed with the help of the ab initio matrix block negative factor counting (NFC) method fo r the DOSs, The neglected effects of the sugar-phosphate chain and the wate r environment (with the counterions) were assessed on the basis of previous ab initio band structure calculations. Further, in the calculation of sing le nucleotide base stacks also basis set and correlation effects have been investigated. In the case of a single strand the level spacing widths of th e allowed regions and the fundamental gap were calculated also with Clement i's double sigma basis and corrected for correlation at the MP2 level. The inverse interaction method was applied for the study of Anderson localizati on. (C) 2000 Elsevier Science B.V. All rights reserved.