Am. Parrott et al., RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour, NUCL ACID R, 28(2), 2000, pp. 489-497
We have probed the effects of altering buffer conditions on the behaviour o
f two aptamer RNAs for the bacteriophage MS2 coat protein using site-specif
ic substitution of 2'-deoxy-2-aminopurine nucleotides at key adenosine posi
tions. These have been compared to the wild-type operator stem-loop oligonu
cleotide, which is the natural target for the coat protein, The fluorescenc
e emission spectra show a position and oligonucleotide sequence dependence
which appears to reflect local conformational changes. These are largely si
milar between the differing oligonucleotides and deviations can be explaine
d by the individual features of each sequence. Recognition by coat protein
is enhanced, unaffected or decreased depending on the site of substitution,
consistent with the known protein-RNA contacts seen in crystal structures
of the complexes. These data suggest that the detailed conformational dynam
ics of aptamers and wild-type RNA ligands for the same protein target are r
emarkably similar.