RECONCILIATION OF THE X-RAY AND NMR STRUCTURES OF THE THROMBIN-BINDING APTAMER D(GGTTGGTGTGGTTGG)

The thrombin-binding aptamer d(GGTTGGTGTGGTTGG) is one of a family of DNA oligonucleotldes that were identified by in vitro selection to bin d specifically and with high affinity to thrombin. Two groups independ ently determined the tertiary structure in solution by NMR and at abou t the same time, the X-ray crystal structure of the aptamer in complex with thrombin was reported. In all cases, the thrombin-binding aptame r was found to fold into a structure containing two planar guanine qua rtets as its core. The NMR and crystal structures, however, have funda mentally different folding patterns owing to differences in the way th ese central bases are connected. We discuss the distinctions between t he refined crystal and solution structures and show that the NMR model is consistent with the X-ray diffraction data. (C) 1996 Academic Pres s Limited