Methods for imaging DNA in liquid with lateral molecular-force microscopy

Shear force microscopy is not normally associated with the imaging of biomolecules in a liquid environment. Here we show that the recently developed scattered evanescent wave (SEW) detection system, combined with custom-designed vertically oriented cantilevers (VOCs), can reliably produce true non-contact images in liquid of DNA molecules. The range of cantilever spring constants for successful shear force imaging was experimentally identified between 0.05 and 0.09 N m(-1). Images of λ-DNA adsorbed on mica in distilled water were obtained at scan rates of 8000 pixels s(-1). A new constant-height force mapping mode for VOCs is also presented. This method is shown to control the vertical position of the tip in the sample plane with better than 1 nm accuracy. The force mode is demonstrated by mapping the shear force above λ-DNA molecules adsorbed on mica in a liquid environment at different tip-sample separations.

Micro-fabricated mechanical sensors for lateral molecular-force microscopy

Atomic force microscopy (AFM) has been very successful in measuring forces perpendicular to the sample plane. Here, we present the advantages of turning the AFM cantilever 90° in order for it to be perpendicular to the sample. This rotation leads naturally to the detection of in-plane forces with some extra advantages with respect to the AFM orientation. In particular, the use of extremely small (1μm wide) and soft (k≅10(-5)N/m) micro-fabricated cantilevers is demonstrated by recording their thermal power spectral density in ambient conditions and in liquid. These measurements lead to the complete characterisation of the sensors in terms of their stiffness and resonant frequency. Future applications, which will benefit from the use of this force microscopy technique, are also described.

Processive behaviour of kinesin observed using micro-fabricated cantilevers

The mechanical characterization of biomolecular motors requires force sensors with sub-piconewton resolution. The coupling of a nanoscale motor to this type of microscale sensors introduces structural deformations in the motor according to the thermally activated degrees of freedom of the sensor. At present, no simple solution is available to reduce these effects. Here, we exploit the advantages of micro-fabricated cantilevers to produce a force sensor with essentially one degree of freedom and a spring constant of 0.03 pN nm(-1) for the study of the molecular motor protein kinesin-1. During processive runs, the cantilever constrains the movement of the cargo binding domain of kinesin in a straight line, parallel to the microtubule track, and excludes specific reaction coordinates such as cargo rotation. In these conditions, we measured a step size of 8.0 ± 0.4 nm and a maximal unloaded velocity of 820 ± 80 nm s(-1) at saturated adenosine triphosphate (ATP) concentration. We concluded that the motor does not need to rotate its tail as it moves through consecutive stepping cycles.

Real-time nanofabrication with high-speed atomic force microscopy

The ability to follow nanoscale processes in real-time has obvious benefits for the future of material science. In particular, the ability to evaluate the success of fabrication processes in situ would be an advantage for many in the semiconductor industry. We report on the application of a previously described high-speed atomic force microscope (AFM) for nanofabrication. The specific fabrication method presented here concerns the modification of a silicon surface by locally oxidizing the region in the vicinity of the AFM tip. Oxide features were fabricated during imaging, with relative tip-sample velocities of up to 10 cm s(-1), and with a data capture rate of 15 fps.