A model of the structure of HOO-Co·bleomycin bound to d(CCAG TACTGG): recognition at the d(GpT) site and implications for double-stranded DNA cleavage

Abstract

Background: The bleomycins (BLMs) are a family of natural products used clinically as antitumor agents. In the presence of their required cofactors, iron and oxygen, BLMs bind to and mediate single-stranded and double-stranded DNA cleavage. Recently, two dimensional nuclear magnetic resonance (2D NMR) spectroscopic studies and molecular modeling have provided a picture of how the hydroperoxide form of cobalt BLM A2 (HOO-CoBLM), an analog of ‘activated’ iron BLM (HOO-FeBLM), binds to a d(GpC) motif and of the basis for both sequence specificity and chemical specificity of DNA cleavage. Results: The solution structure of HOO-CoBLM bound to d(CCAGTACTGG) containing a'hot spot' for double-stranded DNA cleavage at T5 and T15 is reported using constraints from 2D NMR spectroscopy. The mode of binding and basis for sequence specificity and chemical specificity of cleavage is almost identical to that of a d(GpC) motif. This structure has allowed formulation of a structural model for how a single molecule of FeBLM can mediate a double-stranded DNA cleavage event without dissociation from the DNA. Conclusions: The structural similarity of HOO-CoBLM bound to d(GpT) in d(CCAGTACTGG) compared to a d(GpC) motif suggests a general paradigm for the binding of HOO-CoBLM to DNA and, by analogy, for the binding of the biological significant entity 100-FeBLM.