Reconciliation of the X-ray and NMR structures of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG)

Abstract

The thrombin-binding aptamer d(GGTTGGTGTGGTTGG) is one of a family of DNA oligonucleotides that were identified by in vitro selection to bind specifically and with high affinity to thrombin. Two groups independently determined the tertiary structure in solution by NMR and at about the same time, the X-ray crystal structure of the aptamer in complex with thrombin was reported. In all cases, the thrombin-binding aptamer was found to fold into a structure containing two planar guanine quartets as its core. The NMR and crystal structures, however, have fundamentally different folding patterns owing to differences in the way these central bases are connected. We discuss the distinctions between the refined crystal and solution structures and show that the NMR model is consistent with the X-ray diffraction data.