The atomic force microscope (AFM) is a powerful tool for imaging individual biological molecules attached to a substrate and placed in aqueous solution. At present, however, it is limited by the speed at which it can successively record highly resolved images. We sought to increase markedly the scan speed of the AFM, so that in the future it can be used to study the dynamic behavior of biomolecules. For this purpose, we have developed a high-speed scanner, free of resonant vibrations up to 60 kHz, small cantilevers with high resonance frequencies (450 -650 kHz) and small spring constants (150 -280 pN͞nm), an objective-lens type of deflection detection device, and several electronic devices of wide bandwidth. Integration of these various devices has produced an AFM that can capture a 100 ؋ 100 pixel 2 image within 80 ms and therefore can generate a movie consisting of many successive images (80-ms intervals) of a sample in aqueous solution. This is demonstrated by imaging myosin V molecules moving on mica (see http:͞͞www.s.kanazawa-u.ac.jp͞phys͞biophys͞bmvmovie.htm). One of the advantages of the atomic force microscope (AFM) (1) is its capacity to image individual biomolecules in, say, a buffered solution containing ions at physiological concentrations (2, 3). Such capacity suggests that the instrument can be used to record the dynamic behavior of such molecules. In practice, however, only very slow processes can be recorded (2, 4-6), because commercially available AFMs require minutes to form an acceptable image, and many interesting biological processes occur at much higher rates. To understand, and overcome, the factors that limit the scanning rate of an AFM, we begin by considering relations between the characteristics of the constituting components.We consider only the ''tapping mode'' of AFM operation (Digital Instruments, Santa Barbara, CA). This is the mode suitable for imaging biological macromolecules, because vertical oscillation of the cantilever at (or near to) its resonance frequency reduces lateral forces between the tip and the sample (7). The oscillating tip briefly taps the surface at the bottom of each swing, resulting in a decrease in oscillation amplitude. During the x-y scan of the sample stage a feedback loop (see below) keeps this decrease (and hence the tapping force) constant; this is necessary for minimizing the deformation of soft samples. The error signal-the difference between a preset signal and the rms amplitude of the cantilever-is fed into a proportional-integraldifferential (PID) feedback circuit. The PID output is amplified and then sent to the z-piezo actuator; this is repeated until the error signal returns to zero. For the three-dimentional movement of the sample stage to follow the sample topography accurately, the bandwidth of the feedback loop should be comparable to, or larger than, the frequency determined by the x-y scan velocity and the apparent width of the features on the surface. To increase the imaging bandwidth, all elements in the feedback loop have to be optimi...

The dynamic behaviour of myosin V molecules translocating along actin filaments has been mainly studied by optical microscopy. The processive hand-over-hand movement coupled with ATP hydrolysis was thereby demonstrated. However, the protein molecules themselves are invisible in the observations and have therefore been visualised by electron microscopy in the stationary states. Namely, the concomitant assessment of structure and dynamics has been unfeasible, a situation prevailing throughout biological research. Here, using high-speed atomic force microscopy, we directly visualise myosin V molecules walking along actin tracks. themselves. The structure of proteins has been studied by electron microscopy, x-ray crystallography, or NMR but the obtained structures are substantially static. To overcome this long-standing dilemma and enable to simultaneously record the structure and dynamics of functioning biomolecules, high-speed atomic force microscopy (HS-AFM) has been developed [2][3][4][5] . The recent significant improvement in its

High-speed atomic force microscopy (HS-AFM) allows direct visualization of dynamic structural changes and processes of functioning biological molecules in physiological solutions, at subsecond to sub-100-ms temporal and submolecular spatial resolution. Unlike fluorescence microscopy, wherein the subset of molecular events that you see is dependent on the site where the probe is placed, dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules function. Here we present protocols for HS-AFM imaging of proteins in action, including preparation of cantilever tips, step-by-step procedures for HS-AFM imaging, and recycling of cantilevers and sample stages, together with precautions and troubleshooting advice for successful imaging. The protocols are adaptable in general for imaging many proteins and protein-nucleic acid complexes, and examples are described for looking at walking myosin, ATP-hydrolyzing rotorless F(1)-ATPase and cellulose-hydrolyzing cellulase. The entire protocol takes 10-15 h, depending mainly on the substrate surface to be used.

Directly observing individual protein molecules in action at high spatiotemporal resolution has long been a holy grail for biological science. This is because we long have had to infer how proteins function from the static snapshots of their structures and dynamic behavior of optical makers attached to the molecules. This limitation has recently been removed to a large extent by the materialization of high-speed atomic force microscopy (HS-AFM). HS-AFM allows us to directly visualize the structure dynamics and dynamic processes of biological molecules in physiological solutions, at subsecond to sub-100-ms temporal resolution, without disturbing their function. In fact, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. In this review, we first describe theoretical considerations for the highest possible imaging rate of this new microscope, and then highlight recent imaging studies. Finally, the current limitation and future challenges to explore are described.

The CRISPR-associated endonuclease Cas9 binds to a guide RNA and cleaves double-stranded DNA with a sequence complementary to the RNA guide. The Cas9–RNA system has been harnessed for numerous applications, such as genome editing. Here we use high-speed atomic force microscopy (HS-AFM) to visualize the real-space and real-time dynamics of CRISPR-Cas9 in action. HS-AFM movies indicate that, whereas apo-Cas9 adopts unexpected flexible conformations, Cas9–RNA forms a stable bilobed structure and interrogates target sites on the DNA by three-dimensional diffusion. These movies also provide real-time visualization of the Cas9-mediated DNA cleavage process. Notably, the Cas9 HNH nuclease domain fluctuates upon DNA binding, and subsequently adopts an active conformation, where the HNH active site is docked at the cleavage site in the target DNA. Collectively, our HS-AFM data extend our understanding of the action mechanism of CRISPR-Cas9.

Conventional atomic force microscopes (AFMs) take at least 30-60 s to capture an image, while dynamic biomolecular processes occur on a millisecond timescale or less. To narrow this large difference in timescale, various studies have been carried out in the past decade. These efforts have led to a maximum imaging rate of 30-60 ms/ frame for a scan range of~250 nm, with a weak tip-sample interaction force being maintained. Recent imaging studies using high-speed AFM with this capacity have shown that this new microscope can provide straightforward and prompt answers to how and what structural changes progress while individual biomolecules are at work. This article first compares high-speed AFM with its competitor (single-molecule fluorescence microscopy) on various aspects and then describes high-speed AFM instrumentation and imaging studies on biomolecular processes. The article concludes by discussing the future prospects of this cutting-edge microscopy.

In tapping mode atomic force microscopy, the cantilever tip intermittently taps the sample as the tip scans over the surface. This mode is suitable for imaging fragile samples such as biological macromolecules, because vertical oscillation of the cantilever reduces lateral forces between the tip and sample. However, the tapping force ͑vertical force͒ is not necessarily weak enough for delicate samples, particularly for biomolecular systems containing weak inter-or intramolecular interactions. Light tapping requires an amplitude set point ͑i.e., a constant cantilever amplitude to be maintained during scanning͒ to be set very close to its free oscillation amplitude. However, this requirement does not reconcile with fast scans, because, with such a set point, the tip may easily be removed from the surface completely. This article presents two devices to overcome this difficulty; a new feedback controller ͑named as "dynamic proportional-integral-differential controller"͒ and a compensator for drift in the cantilever-excitation efficiency. Together with other devices optimized for fast scan, these devices enable high-speed imaging of fragile samples.

High-speed atomic force microscopy was employed to observe structural changes in actin filaments induced by cofilin binding. Consistent with previous electron and fluorescence microscopic studies, cofilin formed clusters along actin filaments, where the filaments were 2-nm thicker and the helical pitch was ∼25% shorter, compared to control filaments. Interestingly, the shortened helical pitch was propagated to the neighboring bare zone on the pointed-end side of the cluster, while the pitch on the barbed-end side was similar to the control. Thus, cofilin clusters induce distinctively asymmetric conformational changes in filaments. Consistent with the idea that cofilin favors actin structures with a shorter helical pitch, cofilin clusters grew unidirectionally toward the pointed-end of the filament. Severing was often observed near the boundaries between bare zones and clusters, but not necessarily at the boundaries.DOI: http://dx.doi.org/10.7554/eLife.04806.001