TY  - JOUR
AU  - Stafflinger, Helena
AU  - Neißner, Konstantin
AU  - Bartsch, Saskia
AU  - Pichler, Alexander K
AU  - Bartosik, Karolina
AU  - Dhamotharan, Karthikeyan
AU  - Abele, Rupert
AU  - Duchardt-Ferner, Elke
AU  - Micura, Ronald
AU  - Schindelin, Hermann
AU  - Wöhnert, Jens
TI  - Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex
JO  - Nucleic acids symposium series
VL  - 53
IS  - 22
SN  - 0305-1048
CY  - Oxford
PB  - Oxford Univ. Press
M1  - PUBDB-2026-00442
SP  - gkaf1315
PY  - 2025
N1  - DFG) grant WO 901/1-1 (to J.W.), DFG through Grant INST161/816-1 FUGG
AB  - RNA aptamers obtained from in vitro selection experiments provide unique insights into the structural properties and ligand recognition capabilities of RNA in general. In order to investigate the relationships between RNA sequence information content and structural complexity with ligand affinity and specificity, the Szostak group previously identified eleven different families of GTP-binding aptamers varying widely in their sequence conservation patterns as well as in their secondary structure complexity and topology. The class V GTP aptamer has a particularly high affinity for GTP. Here, we report the high-resolution X-ray crystal structure of this aptamer–GTP complex. Remarkably, GTP is found to be integrated into one layer of a two-layered G-quadruplex, thereby rationalizing the high ligand affinity and the observed specificity. The G-quadruplex is extended on one side by a noncanonical tetrad layer containing three non-G nucleotides and on the other side by a Watson–Crick base pair stacking on top of an unpaired adenine. Interestingly, the G-nucleotides forming the G-quadruplex originate from two asymmetric bulges separated by an 8 base pair A-form helix, resulting in a complex and previously unobserved G-quadruplex topology.
LB  - PUB:(DE-HGF)16
DO  - DOI:10.1093/nar/gkaf1315
UR  - https://bib-pubdb1.desy.de/record/644609
ER  -