Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches.
The adenine-specific pbuE riboswitch undergoes metal ion-dependent folding that involves a long-range tertiary loop-loop interaction between two stem loops. Fluorescence resonance energy transfer (FRET) and single-molecule FRET studies demonstrate the ability of the loops to interact in the absence of the ligand. Although the riboswitch can fold in the absence of adenine, ligand binding stabilizes this folded conformation by increasing the folding and decreasing the unfolding rates of the riboswitch. The presence of the ligand also decreases the magnesium ion concentration required to promote the loop-loop interaction. Single-molecule FRET studies demonstrate that individual aptamer molecules exhibit great heterogeneity in the rates of folding and unfolding, which is reduced in the presence of adenine. Moreover, single-molecule FRET proposes that riboswitch folding proceeds through a complex landscape that involves a discrete intermediate.
Lemay
Jean-François
JF
Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1.
Penedo
J Carlos
JC
Mulhbacher
Jérôme
J
Lafontaine
Daniel A
DA
D000225:Adenine / Q000378:metabolism*; D001483:Base Sequence; D004591:Electrophoresis, Polyacrylamide Gel; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes / Q000378:metabolism; D005786:Gene Expression Regulation; D008967:Molecular Biology / Q000379:methods*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics; D013194:Staining and Labeling
D005456:Fluorescent Dyes; D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D000225:Adenine