The small family of natural products that include the duocarmycins, yatakemycin, and CC-1065 incorporates a remarkable combination of molecular features integrated into their compact structures controlling their DNA binding and ensuing alkylation reaction and their resulting exceptionally potent biological activity. The systematic total syntheses of an extensive series of analogues containing deep-seated structural changes have been utilized to define subtle relationships between structure, reactivity, reaction regioselectivity, and biological potency using fundamental chemical principles. Superimposed on a skeleton that selectively binds DNA minor groove AT-rich sequences (shape-selective recognition), the compounds incorporate a spirocyclopropylcyclohexadienone whose reactivity has been masked by a cross-conjugated and remarkably stabilizing vinylogous amide, taming what would ordinarily be an exceptionally reactive electrophile. We have suggested that disruption of this vinylogous amide conjugation through a DNA binding-induced conformational change activates the cyclopropane for a stereoelectronically controlled nucleophilic attack serving as the catalysis for the DNA alkylation reaction (shape-dependent catalysis). These studies highlight the remarkable design that nature utilized to mask a reactive electrophile that is subsequently capable of selective activation by a unique mechanism upon reaching its biological target (target-based activation). In addition to elucidating the mechanism of activation of these natural products, a detailed understanding of the relationship between intrinsic reactivity and biological potency resulted from studying analogues with deep-seated structural modifications. These studies defined a fundamental parabolic relationship between chemical reactivity and biological potency (cytotoxic activity) and identified the optimal balance between reactivity and stability, reflecting a stability required to effectively reach their biological target in a biological milieu while maintaining a sufficient reactivity to effectively alkylate DNA once they do. Remarkably, but perhaps not surprisingly, duocarmycin SA and yatakemycin incorporate an alkylation subunit that lies at the pinnacle of this relationship, reflecting nature's exquisite optimization of their DNA alkylation properties. Unique insights into nature's potential steps in this evolutionary optimization were revealed with the discovery of an alternative but less productive indole N5 H spirocyclization of duocarmycin SA lacking a C4-phenol. Finally, as a result of the increased understanding of these compounds (reactivity vs potency), we described the rational design of a synthetic alkylation subunit (CTI) incorporating a single skeletal atom change that maintains the DNA alkylation properties of its parent natural product (CC-1065) but exhibited a greater chemical stability and resulting increased biological potency. This remarkably stable alkylation subunit analogue lies at the pinnacle of the parabolic relationship and constitutes one of the most stable derivatives to be characterized to date.