Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342.

Abstract

O6‐ethyl‐G (e6G) is an important DNA lesion, caused by the exposure of cells to alkylating agents such as N‐ethyl‐N‐nitrosourea. A strong correlation exists between persistence of e6G lesion and subsequent carcinogenic conversion. We have determined the three‐dimensional structure of a DNA molecule incorporating the e6G lesion by X‐ray crystallography. The DNA dodecamer d(CGC[e6G]AATTCGCG), complexed to minor groove binding drugs Hoechst 33258 or Hoechst 33342, has been crystallized in the space group P212121, isomorphous to other related dodecamer DNA crystals. In addition, the native dodecamer d(CGCGAATTCGCG) was crystallized with Hoechst 33342. All three new structures were solved by the molecular replacement method and refined by the constrained least squares procedure to R‐factors of approximately 16% at approximately 2.0 A resolution. In the structure of three Hoechst drug‐dodecamer complexes in addition to the one published earlier [Teng et al. (1988) Nucleic Acids Res., 16, 2671–2690], the Hoechst molecule lies squarely at the central AATT site with the ends approaching the G4‐C21 and the G16‐C9 base pairs, consistent with other spectroscopic data, but not with another crystal structure reported [Pjura et al. (1987) J. Mol. Biol., 197, 257–271]. The two independent e6G‐C base pairs in the DNA duplex adopt different base pairing schemes. The e6G4‐C21 base pair has a configuration similar to a normal Watson‐Crick base pair, except with bifurcated hydrogen bonds between e6G4 and C21, and the ethyl group is in the proximal orientation. In contrast, the e6G16‐C9 base pair adopts a wobble configuration and the ethyl group is in the distal orientation.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of DNA Recognition by the Human UV-damaged DNA-binding Protein

“…On the other hand, no global conformation change due to 8-oxo-G was observed in NMR and circular dichroism studies (51,52). There was no bending in the crystal structures of dodecamer duplexes containing an O 6 -ethylguanine⅐cytosine pair, although they were complexed with minor groove binding drugs (53,54), and even when O 6 -Me-G was opposite adenine, the overall structure of this mispaired dodecamer duplex was very close to that of the parent duplex (55). NMR studies of duplexes containing a T⅐T mismatch (56) and a nick (57) revealed that these lesions had little influence on the conformation of the normal B-form DNA.…”

Specific binding of hoechst 33258 to the d(CGCAAATTTGCG)2 duplex: calorimetric and spectroscopic studies

“…The change in surface area on binding, ÁA, is the difference between the area of the complex and the summed surface areas for the drug-free native duplex and the ligand molecule separated from each complex. High-resolution crystal coordinates are not available for the free dye, but comparison with the ligands separated from other DNA-Hoechst 33258 crystal structures (Pjura et al, 1987;Teng et al, 1988;Quintana et al, 1991;Sriram et al, 1992) showed only $2 to 3% variation in surface areas for the bound molecules. Similarly, calculated areas for a minimized model ligand constructed using standard bond and angle geometries differed by <2% from the experimental DNA-bound values.…”

“…Both high-®eld solution NMR and X-ray crystallographic methods have been used to examine the complexes formed between Hoechst 33258 and a variety of oligonucleotides (Pjura et al, 1987;Teng et al, 1988;Parkinson et al, 1990;Searle & Embrey, 1990;Fede et al, 1991;Quintana et al, 1991;Sriram et al, 1992). Thus, structural studies with the 12-mer d(CGCGAATTCGCG) 2 duplex reveal a 1:1 binding stoichiometry with the bound ligand positioned in the minor groove AT-tract.…”

Intrinsic Conformational Preferences of the Hoechst Dye Family and their Influence on DNA Binding

“…It is an N-methyl piperazine derivative with two benzimidazole groups and one phenol group. Many structural variants of Hoechst 33258 have been synthesized in order to modify the AT selectivity using chemical changes in benzimidazole systems (Sriram et al, 1992;Bailly et al, 1994). Chemical modifications in the phenol group have also been performed to add additional sequence-determining features to the ends of the molecule (Ebrahimi et al, 1992;Parkinson et al, 1994).…”