STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG)

We have determined the structure of the synthetic DNA octamer d(pCpCpC pGpCpGpGpG) in five different crystal forms by single crystal X-ray di ffraction. One crystal belongs to the space group P4(3)2(1)2 with a=b= 41.77, c=25.15 Angstrom, whereas all others have the space group P2(1) 2(1)2(1) with progressively decreasing unit cell volumes. In all cryst als the octamer forms duplexes of A-DNA and all crystals display a sim ilar packing mode, typical for A-DNA. The structure of the duplex vari es from loose to very compact when going from one crystal form to anot her. The mast compact form exhibits a volume of 995 Angstrom(3) per ba se pair. Such a high density has never been found in A-DNA, being more characteristic of Z-DNA crystals. A comparison of the most with the l east compact forms gives a RMS value of 1.7 Angstrom, with the distanc e between the phosphate centers through the major groove being almost twice shorter in the compact form. The phosphate-phosphate separation across the major groove in the compact form is extremely small, 0.7 An gstrom. The helical parameters also vary significantly in the various crystal forms. Differences in the helical twist can reach 13 degrees i n the same step of the octamer in different crystal forms. The results prove that A-DNA is structurally very variable and demonstrate that t he local structure of the same DNA fragment can strongly depend on the crystal environment.