Imaging unlabeled proteins on DNA with super-resolution.

Fluorescence microscopy is invaluable to a range of biomolecular analysis approaches. The required labeling of proteins of interest, however, can be challenging and potentially perturb biomolecular functionality as well as cause imaging artefacts and photo bleaching issues. Here, we introduce inverse (super-resolution) imaging of unlabeled proteins bound to DNA. In this new method, we use DNA-binding fluorophores that transiently label bare DNA but not protein-bound DNA. In addition to demonstrating diffraction-limited inverse imaging, we show that inverse Binding-Activated Localization Microscopy or 'iBALM' can resolve biomolecular features smaller than the diffraction limit. The current detection limit is estimated to lie at features between 5 and 15 nm in size. Although the current image-acquisition times preclude super-resolving fast dynamics, we show that diffraction-limited inverse imaging can reveal molecular mobility at ∼0.2 s temporal resolution and that the method works both with DNA-intercalating and non-intercalating dyes. Our experiments show that such inverse imaging approaches are valuable additions to the single-molecule toolkit that relieve potential limitations posed by labeling.

Kinesin's step dissected with single-motor FRET.

The motor protein Kinesin-1 drives intracellular transport along microtubules, with each of its two motor domains taking 16-nm steps in a hand-over-hand fashion. The way in which a single-motor domain moves during a step is unknown. Here, we use Förster resonance energy transfer (FRET) between fluorescent labels on both motor domains of a single kinesin. This approach allows us to resolve the relative distance between the motor domains and their relative orientation, on the submillisecond timescale, during processive stepping. We observe transitions between high and low FRET values for certain kinesin constructs, depending on the location of the labels. These results reveal that, during a step, a kinesin motor domain dwells in a well-defined intermediate position for approximately 3 ms.

Alternating-site mechanism of kinesin-1 characterized by single-molecule FRET using fluorescent ATP analogues.

Kinesin-1 motor proteins move along microtubules in repetitive steps of 8 nm at the expense of ATP. To determine nucleotide dwell times during these processive runs, we used a Förster resonance energy transfer method at the single-molecule level that detects nucleotide binding to kinesin motor heads. We show that the fluorescent ATP analog used produces processive motility with kinetic parameters altered <2.5-fold compared with normal ATP. Using our confocal fluorescence kinesin motility assay, we obtained fluorescence intensity time traces that we then analyzed using autocorrelation techniques, yielding a time resolution of approximately 1 ms for the intensity fluctuations due to fluorescent nucleotide binding and release. To compare these experimental autocorrelation curves with kinetic models, we used Monte-Carlo simulations. We find that the experimental data can only be described satisfactorily on the basis of models assuming an alternating-site mechanism, thus supporting the view that kinesin's two motor domains hydrolyze ATP and step in a sequential way.