NMR studies of the hydroperoxide form of cobalt deglycoBleomycin A2 (HOO-CodGBLM) and its complex with oligonucleotide d(CCAGGCCTGG) (1, C is the site of cleavage) are presented in an effort to establish deglycoBLM as a prototype for studies with BLM analogues, synthesized without the sugar moieties (Boger et al. Bioorg. Med Chem. 1995, 3, 1281-1295). The structure determination of free HOO-CodGBLM has been hampered by the lack of NOE or ROE information. By direct comparison of the chemical shifts and coupling constants of HOO-CodGBLM with its glycosylated parent HOO-CoBLM, the former is shown to share many global structural features with the latter, including the nature of axial Ligands (a point recently disputed by Caceres-Cortes et al. fur. J. Biochem. 1997, 244, 818-828), the screw sense of metal-coordinating ligands, and the folding of the peptide linker region. The structure of HOO-CodGBLM bound to 1 is reported based on molecular modeling using NMR constraints (39 intermolecular and 44 intramolecular NOEs). The intercalative mode of binding of the bithiazole tail 3＇ to the cleavage site at C6, the sequence specific recognition of guanine 5＇ to the cleavage site by the pyrimidine of HOO-CodGBLM, and the proximity of the hydroperoxide Ligand to the 4＇ hydrogen of the cleavage site are almost identical to those previously reported for HOO-CoBLM bound to 1 (Wu et al. J. Am. Chem. Sec. 1996, 118, 1281-1294). The general conformity between the two structures provides strong support for a similar coordination environment of the cobalt and a structural basis for the observed similarity in the DNA cleavage specificity at GPy sites by BLM and deglycoBLM. However, observation of minor complex(es), selective broadening of certain protons associated with the A3.T18 base pair, a K-d for 1 of 5.9 mu M, 35-fold greater than its parent, and an altered ratio of single strand to double strand cleavage, define the importance of the sugars＇ nonspecific interactions with DNA to the efficiency and selectivity of cleavage.