X-ray Structure of a Lectin-bound DNA Duplex Containing an Unnatural Phenanthrenyl Pair

The reluctance of DNA duplexes containing unnatural base-pair surrogates to yield crystal of sufficient quality and the inherent difficulty to overcome the phasing problem in the structure resolution, are well-known difficulties in the field of nucleic acid research. One way of overcoming this difficulty is to induce both conformational and packing stability throughout binding the DNA-like polymer to a template prompt to “robust” crystalline arrangements. Lectins in their propensity to yield high quality crystalline arrangements can serve as templates to solve the structures of (macro) molecules that are difficult to crystallize. Such a concept was successfully demonstrated throughout the X-ray crystal structure resolution of a DNA 13-mer duplex incorporating a phenanthrenyl pair in the center of the helix and carrying an L-alpha-fucose analogue.

This construct was designed to bind to the fucose specific Pseudomonas aeruginosa lectin LecB (also called PA-IIL). A high-resoltion data set was collected and the structure of the DNA part of the macromolecular complex was solved at a resolution of 2 ;9 Ang. Delivering important structural information.