Atomic force microscopy (AFM, also called scanning force microscopy) is proving to be a useful technique for imaging DNA. Thus it is important to push the limits of AFM imaging in order to explore both what types of DNA can be reliably imaged and identified and also what substrates and methods of sample preparation are suitable. The following advances in AFM of DNA are presented here. (i) DNA molecules as short as 25 bases can be seen by AFM. The short single-stranded DNAs imaged here (25 and 50 bases long) appeared globular in the AFM, perhaps because they are all capable of intramolecular base pairing and because the DNAs were in a Mg(ll) buffer, which facilitates intramolecular cross-bridging. (ii) AFM images in air of short double-stranded DNA molecules, 100-200 bp, gave lengths consistent with A-DNA. (iii) AFM images of poly (A) show both short bent lumpy molecules with an apparent persistence length of 40 nm and long straight molecules with an apparent persistence length of 600 nm. For comparison, the apparent persistence length for double-stranded DNA from phX-174 under the same conditions was 80 nm. (iv) Structures believed to be triple- stranded DNA were seen in samples of poly(dA.poly(dT) and poly (dG).poly(dC). These structures were twice as high as double-stranded DNA and the same width. (v) Entire molecules of lambda DNA, approx. 16 micron long, were imaged clearly in overlapping scans. (vi) Plasmid DNA was imaged on oxidized silicon, although less clearly than on mica.

Tapping mode atomic force microscopy (AFM), also known as amplitude modulated (AM) or AC mode, is a proven, reliable and gentle imaging mode with widespread applications. Over the several decades that tapping mode has been in use, quantification of tip-sample mechanical properties such as stiffness has remained elusive. Bimodal tapping mode keeps the advantages of single-frequency tapping mode while extending the technique by driving and measuring an

Observations of intact reconstituted and native collagen fibres were performed with the atomic force microscope. The results are compared between the two types of fibres and with those obtained previously with the electron microscope on freeze-etched or negative stained samples. Some of the findings presented here indicate that the specimens observed in air with the atomic force microscope were still in a hydrated state.

We have constructed a fluid cell for an atomic force microscope that operates in tapping mode using either an oscillating piezo or magnetic drive. This fluid cell allows direct comparison of the image quality using the two drive mechanisms over identical areas of a sample without fluid or cantilever exchange. We found that the magnetically driven cantilever's tuning curve was very similar to the thermal noise power spectrum, allowing an accurate determination of the cantilever resonance frequency. This is in contrast to the piezo driven tuning curve, which contained a number of peaks that appeared to be a convolution of the true cantilever resonance with the complicated acoustic spectrum of the fluid cell. We imaged two biologically relevant samples: DNA molecules and liquid phase phospholipid bilayers. For both samples, we found that the image quality, as measured by feature height, lateral resolution, and image stability, was independent of the drive method. This suggests that, despite the apparent differences in the frequency response, the physical motion of the cantilever tip, when it is driven near its resonance frequency, is the same for both driving mechanisms.