Manipulative interplay of the interstrand cross-linker Bizelesin with d(TAATTA)₂ to achieve sequence recognition of DNA

As expected, Bizelesin, which is a biscyclopropa[c]pyrrolo[3,2-e]indol-4(5H)-one [(+)-CPI]-derived DNA-DNA cross-linker, has a high interstrand cross-linking reactivity with the palindromic sequence 5'-d(CGTAATTȦCG)₂. Contrary to expectations, the target duplex is rearranged to yield two products: one (major product) contains an AT step wherein both adenines are syn-oriented and hydrogen bonded to thymines forming a stable Hoogsteen base-paired region flanked by Watson-Crick base-paired regions (5HG); the other (minor product) contains anti-oriented AT-step adenines that show no evidence of hydrogen bonding with pairing thymines (5OP) in an otherwise normally base-paired duplex. In another unexpected outcome, the reaction of two 'uncoupled' monoalkylating (+)-CPI 'halves' of Bizelesin with the same duplex alkylates same-strand adenines three base pairs apart [5'-d(CGTAȦTTȦCG)₂] rather than the anticipated opposite-strand adenines six base pairs apart (which would mimic Bizelesin). To probe the molecular mechanism that leads to Bizelesin's unusual DNA rearrangement, which appears to be a requirement for DNA-DNA interstrand cross-linking, we have carried out conformational exchange analyses (NOESY and ROESY) and restrained molecular dynamics simulations of these adducts. These studies suggest that Bizelesin controls the rearrangement of the six-base-pair target prior to cross-linkage and restricts the cross-linked DNA adduct's range of motion, freezing-out adduct conformers defined by alternative drug-DNA hydrogen-bond regimes. The two competing cross-linkage pathways share a common first step, the opening of the central AT-step base pairs, an event that is facilitated by the energetics of monoadduct-induced DNA bending distortion. One pathway (to 5HG) stabilizes these open bases by reorganizing the AT-step region into two Hoogsteen base pairs, the thymine bases of which also hydrogen bond with Bizelesin's ureadiyl subunit. A second pathway (to 5OP) directly stabilizes the open bases by forming a hydrogen-bonding complex between the AT-step thymines and Bizelesin's ureadiyl subunit. Cross-linked DNA motion drives both of the 5HG and 5OP adducts from one ephemeral hydrogen-bonding regime to another, a process documented in the NOESY conformational exchange data and simulated in restrained molecular dynamics trajectories. These results, together with the analysis of other six-base-pair Bizelesin cross-linked species, suggest a novel mechanism for sequence recognition by this cross-linker where monoalkylation distortive stress associated with a bent DNA conformation must be dissipated by a cooperative interaction between drug and duplex to produce a straight B-form-like structure before cross-linking can proceed. This example provides a new mechanism for DNA sequence recognition involving a 'drug-induced rearrangement' of DNA that critically depends upon the interplay of drug and sequence recognition elements.