We have examined the oxidation of oligodeoxynucleotides (ODN) containing various guanine (G)containing sequences with Co(II) ion and benzoyl peroxide (BPO). Sequence-dependent G-cleavage has been observed for double-stranded ODN as revealed by PAGE analysis of the reaction mixture after hot piperidine treatment, whereas non-selective equal G cleavage was observed for single-stranded ODN. The relative rates of sequence-dependent G oxidation were determined by densitometric assay of the DNA cleavage bands. We then performed ab initio calculations of HOMOs of the G-containing sequences with B-form geometry at the HF/6-31G* level. Experimentally observed relative rates of G oxidation matched well with the calculated HOMOs of the G-containing sequences. Thus, the DNA cleavage data obtained from the oxidation of duplex ODNs with Co(II) ion in the presence of BPO correlated nicely with calculated HOMOs, implying that the co(II) ion is coordinated more strongly to the G having a larger HOMO. These results suggest that the coordination of Co(II) ion to the N-7 Of guanine base in a duplex DNA is a HOMO-controlled process, in accordance with the previous NMR studies: on the sequence-dependent binding of Co(II) ion to the N-7 Of guanine base of duplex ODN. After performing ab initio calculations of a number of G-containing sequences, we found important general trends that represent the distribution of HOMOs of G bases in B-form DNA. The results of HOMO mapping described here are extremely important for predicting: (i) which G-sites are more susceptible to electrophilic attack in chemical and biological reactions, such as DNA alkylation by antitumor drugs or mutagens, and (ii) which G-sites are more prone to HOMO-LUMO interactions with DNA-binding drugs and proteins. These results provide a new tool for probing the heterogeneity of DNA sequences.