A DNA DECAMER WITH A STICKY END - THE CRYSTAL-STRUCTURE OF D-CGACGATCGT

The crystal structure of d-CGACGATCGT has been determined to a resolut ion of 2.6 Angstrom. The molecule was synthesized by standard phosphor amidite procedures, and purified by anion-exchange HPLC. Crystals are monolclinic, space group P2(1), with unit cell dimensions, a=26.45 Ang strom, b=34.66 Angstrom, c=32.17 Angstrom, beta=113.45 degrees and Z=4 , containing a B-DNA double helix in each crystallographic asymmetric unit. The structure was solved using molecular replacement, aided by a n isomorphous derivative, in which a bromine atom was attached to the 5 position of cytosine 8. Problems of fit between the search model and the structure ultimately obtained necessitated the use of Patterson c orrelation procedures between the determination of the orientation and the translation of the molecule. In all, 69 solvent molecules have be en identified, and the structure has been refined to an R-factor of 0. 214, using the 1421 reflections with F > 2 sigma(F), collected at -120 degrees C. The sequence produces a molecule containing eight Watson-C rick base-pairs and a two-nucleotide 5'-sticky end at each end of the duplex. The sticky ends cohere with one another, so the molecules form continuous 10-fold double helices throughout the crystal, with each s trand being interrupted by inherent staggered nicks. The relative angu lar relationships between helices in the structure differ from each ot her; most of the arrangements differ from Holliday junctions, whose ro tational orientations are phased by a crossover and which are modeled to contain double helices that are exactly parallel or antiparallel. H owever, one helical juxtaposition in this crystal is similar to the al ignment of double helices in parallel Holliday junctions. A survey of DNA decamers that also form infinite helices in crystals reveals relat ionships that approximate both parallel and antiparallel Holliday junc tion alignments. (C) 1997 Academic Press Limited.