RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour

Citation
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
Citations number
31
Categorie Soggetti
Biochemistry & Biophysics
Journal title
NUCLEIC ACIDS RESEARCH
ISSN journal
03051048 → ACNP
Volume
28
Issue
2
Year of publication
2000
Pages
489 - 497
Database
ISI
SICI code
0305-1048(20000115)28:2<489:RAFTMB>2.0.ZU;2-Q
Abstract
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.