RNA aptamers directed against release factor 1 from Thermus thermophilus.
An in vitro selection/amplification (SELEX) was used to generate RNA aptamers that specifically bind Thermus thermophilus release factor 1 (RF1). From 31 isolated clones, two groups of aptamers with invariable sequences 5'-ACCU-3' and 5'-GAAAGC-3' were isolated. Chemical and enzymatic probing of the structure indicate that in both groups the invariable sequences are located in single-stranded regions of hairpin structures. Complex formations between RF1 and aptamers of both groups were identified by electrophoretic shift assay and chemical footprinting. Deletion of the invariable sequences did not effect the secondary structure of the aptamers but abolished their binding to RF1. RNA motifs matching the invariable sequences of the aptamers are present as consensus sequences in the peptidyl transferase center of 23S rRNAs. T. thermophilus RF1 recognizes UAG stop codons in an Escherichia coli in vitro translation system. Aptamers from both groups inhibited this RF1 activity.
Szkaradkiewicz
Karol
K
Laboratorium für Biochemie, Universität Bayreuth, Universitätsstrasse 30, D-95440, Bayreuth, Germany.
Nanninga
Matthias
M
Nesper-Brock
Martina
M
Gerrits
Michael
M
Erdmann
Volker A
VA
Sprinzl
Mathias
M
D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins; D009690:Nucleic Acid Conformation; D010454:Peptide Termination Factors / Q000378:metabolism*; D014176:Protein Biosynthesis / Q000502:physiology; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D016963:Thermus thermophilus / Q000235:genetics / Q000378:metabolism*
D029968:Escherichia coli Proteins; D010454:Peptide Termination Factors; D012329:RNA, Bacterial; C489005:prfA protein, E coli