Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics.
Many studies of RNA folding and catalysis have revealed conformational heterogeneity, metastable folding intermediates, and long-lived states with distinct catalytic activities. We have developed a single-molecule imaging approach for investigating the functional heterogeneity of in vitro-evolved RNA aptamers. Monitoring the association of fluorescently labeled ligands with individual RNA aptamer molecules has allowed us to record binding events over the course of multiple days, thus providing sufficient statistics to quantitatively define the kinetic properties at the single-molecule level. The ligand binding kinetics of the highly optimized RNA aptamer studied here displays a remarkable degree of uniformity and lack of memory. Such homogeneous behavior is quite different from the heterogeneity seen in previous single-molecule studies of naturally derived RNA and protein enzymes. The single-molecule methods we describe may be of use in analyzing the distribution of functional molecules in heterogeneous evolving populations or even in unselected samples of random sequences.
Elenko
Mark P
MP
Program in Biological and Biomedical Sciences, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA.
Szostak
Jack W
JW
van Oijen
Antoine M
AM
D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001665:Binding Sites; D005456:Fluorescent Dyes / Q000737:chemistry*; D006160:Guanosine Triphosphate / Q000737:chemistry*; D007091:Image Processing, Computer-Assisted; D007700:Kinetics; D008024:Ligands; D013194:Staining and Labeling
D052157:Aptamers, Nucleotide; D005456:Fluorescent Dyes; D008024:Ligands; D006160:Guanosine Triphosphate