Through a comparative analysis of the reactivity and DNA cleaving activity of neocarzinostatin (NCS) chromophore (1) and the corresponding aglycon (2), we show that the carbohydrate residue (aminoglycoside) of 1 both accelerates the rate and improves the efficiency of DNA cleavage versus the aglycon (2), but does not appear to be a major determinant of the base specificity of DNA cleavage by 1. This stands in contrast to earlier findings with another enediyne antibiotic, calicheamicin gamma(1), where the carbohydrate residue was found to be a major determinant of the sequence specificity of DNA cleavage, in addition to playing a functional role in the reductive activation step. Thiol addition experiments with NCS aglycon (2) provide further evidence that the carbohydrate amino group of 1 functions as an internal base in the first step leading to DNA cleavage, thiol. activation. Evidence is also presented supporting the proposal that NCS aglycon (2) is bound tightly and reversibly by the neocarzinostatin binding protein (apo-NCS) and that this binding stabilizes the aglycon in solution.