RESOLUTION ENHANCEMENTS BY TRIPLE HELIX FORMATION. THE CRYSTAL STRUCTURE OF THE D(GGCCAATTGG) - DAPI COMPLEX AT 1.9 A

Dominique Vlieghe & Luc Van Meervelt

Laboratorium voor Macromoleculaire Structuurchemie, K. U. Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium, Dominique.Vlieghe@chem.kuleuven.ac.be

Keywords: DNA, DAPI, minor groove binder, triple helix, DNA-drug interaction

An appropriate choice of the nucleotide sequence containing overhanging nucleotides can lead to the formation of triple helical fragments in the crystal packing [1,2]. We have previously reported that this tight packing is partly responsible for the resolution enhancement to 1.15 A observed in the crystal structure of d(GGCCAATTGG) [3]. The presence of the narrow minor groove in the central d(AATT) sequence suggested that this sequence could be used to improve the resolution of DNA-minor groove binder complexes, currently limited to about 2.2 A.

We now complexed the decamer d(GGCCAATTGG) with the minor groove binder 4',6-diamidino-2-phenylindole (DAPI) and determined its structure at 1.9 A. This relatively high resolution enabled us to rigorously determine the position and orientation of the drug. A novel off-centred binding is observed, with a hydrogen bond between the drug and a GC base pair flanking the AATT segment. In contrast to the previous 2.5 A DAPI-DNA complex structure [4], the drug is not flat and its shape follows more the inherent curvature of the minor groove of the DNA duplex. The structure was refined to completion using SHELXL-93. The final residual factor R was 18.0% for 3562 reflections with Fs > 4s (Fo). At this stage, 81 water molecules were located.

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