Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)₂duplex

Abstract

The bis-benzimidazole drug Hoechst 33258 has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The structure has been solved by molecular replacement and refined to an R factor of 18.5% for 2125 reflections collected on a Xentronics area detector. The drug is bound in the minor groove, at the five base-pair site 5'-ATTTG and is in a unique orientation. This is displaced by one base pair in the 5' direction compared to previously-determined structures of this drug with the sequence d(CGCGAATTCGCG)2. Reasons for this difference in behaviour are discussed in terms of several sequence-dependent structural features of the DNA, with particular reference to differences in propeller twist and minor-groove width.

Synthesis, DNA-Binding Activity and Cytotoxicity of Carbamate Derivatives of Hoechst 33258 in Breast Cancer MCF-7 Cells.

“…3,4) Although various factors are known to be responsible for minor groove binding, their importance can vary from ligand to ligand and no simple rules have emerged yet. Moreover, the dependence of binding specificity of particular ligands on length, sequence composition and flanking regions of the AT tract is widely unexplored.…”

“…1,2) Several high resolution crystal and NMR structures have been determined for these ligands bound to short oligonucleotides and provide valuable insights into the details of their interaction. 3,4) The Hoechst 33258 is bound in the minor groove, with the planar benzimidazole groups oriented parallel to the groove direction and each inner-facing nitrogen atom hydrogen bonding in a bifurcated manner to a pair of adjacent hydrogen bond donors on the edge of the AT base pairs of DNA. 3,4) The structure of the bound drug shows that the bulky piperazine ring is located in a GC region, with the minor groove observed to be wider at this sequence.…”

Crystal structures of nucleic acids and their drug complexes

“…23), extending over three base pairs in total. [131][132][133] The analogue with three linked benzimidazole groups 134 follows the same pattern of hydrogen bonding, with now three pairs of hydrogen bonds, covering four A·T base pairs. This ligand has an overall binding site of ca.…”

Comparison of the binding stoichiometries of positively charged DNA-binding drugs using positive and negative ion electrospray ionization mass spectrometry

“…One of the DNA strands used in this study contained a central AAATA sequence that is a high affinity site for Hoechst 33258 and distamycin [21,22]. Two relatively GC-rich DNA strands (D1 and D3) were also used, which were therefore not predicted to favor the minor groove-binding mode of interaction with dsDNA.…”