Interacting RNA species identified by combinatorial selection.
RNA molecules were selected from a random sequence library for their ability to bind to an RNA stem-loop target. Oligonucleotides with extensive Watson-Crick complementarity to the RNA ligand were selected against by inclusion of a blocking oligodeoxynucleotide in the binding phase of the selection protocol. After 18 generations of SELEX (systematic evolution of ligands by exponential enrichment) a single RNA family was predominant in the binding population. The winning aptamer RNA bound the target RNA with an apparent Kd = 70 nM. Structural mapping and Fe(II)-EDTA protection indicated that the target RNA interacted with small unpaired loops in the aptamer structure.
Cho
B
B
Department of Biochemistry, University of Missouri-Columbia 65212, USA.
Taylor
D C
DC
Nicholas
H B
HB
Schmidt
F J
FJ
D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D018076:DNA, Complementary / Q000378:metabolism; D004722:Endoribonucleases / Q000378:metabolism; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000378:metabolism*; D016337:RNA, Catalytic / Q000378:metabolism; D043262:Ribonuclease P; D013329:Structure-Activity Relationship
D018076:DNA, Complementary; D008024:Ligands; D016337:RNA, Catalytic; D012313:RNA; D004722:Endoribonucleases; D043262:Ribonuclease P