Factors Affecting DNA-DNA Interstrand Cross-Links in the Antiparallel 3 '-3 ' Sense: A Comparison with the 5 '-5 ' Directional Isomer

Abstract

Reported herein is a study of the unusual 3'-3' 1,4-GG interstrand cross-link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen-bonding effects the closely related compounds [{trans-PtCl(NH3)(2)}(2)(mu-trans-Pt(NH3)(2)-{NH2(CH2)(6)NH2}(2))](4+) (BBR3464, 1), [{trans-PtCl(NH3)(2)}(2)(mu-NH2(CH2)(6)-NH2)](2+) (BBR3005, 2), [{trans-PtCl(NH3)(2)}(2)(mu-H2N(CH2)(3)NH2(CH2)(4))](3+) (BBR3571, 3) and [{trans-PtCl(NH3)(2)}(2)-{mu-H2N(CH2)(3)-N(COCF3)(CH2)(4)}](2+) (BBR3571-COCF3, 4) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20-base-pair duplexes. In the "hybridisation directed" method the monofunctionally adducted top strands were hybridised with their complementary 5'-end labelled strands; after 24 h the efficiency of interstrand cross-linking in the 5'-5' direction was slightly higher than in the 3'-3' direction. The second method involved "postsynthetic modification" of the intact duplex; significantly less cross-linking was observed, but again a slight preference for the 5'-5' duplex was present. 2D [H-1, N-15] HSQC NMR spectroscopy studies of the reaction of [N-15]-1 with the sequence 5'-d{TATAC-ATGTATA}(2) allowed direct comparison of the stepwise formation of the 3'-3' IXL with the previously studied 5'-5' IXL on the analogous sequence 5'-d(ATATGTACATAT)(2), Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3'-3' 1,4-GG IXL, but numerous crosslinked adducts formed. Similar results were found for the reaction with the di-nuclear [N-15]-2. Molecular dynamics simulations for the 3'-3' IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.