One of the big advantages of AFM for the structural analysis of biological samples is that it can image
non-conducting surfaces in both air and liquid environments. Unsurprisingly, soon after its invention the
AFM was applied to the analysis of many biological systems, including membrane proteins, DNA and
RNA, protein–nucleic acid complexes and even more complex structures such as chromosomes.
To date, many investigations of nucleic acids have been performed using AFM.38,39By recording a series
of images over a certain period of time, AFM is also able to provide dynamic information on processes
involving nucleic acids, as well as time-lapse AFM movies of processes such as DNA condensationand the
processing and/or degradation of DNA by enzymes such as the endonuclease EcoKI. The level of attainable
image speed in conventional AFM imaging (normally 30–60s per image) has been a major problem, however,
for the imaging of such dynamic events. To a certain extent, this problem has been overcome recently by using
448 Chapter 11
Figure 11.15 (a) Schematic of the principle features of an AFM instrument. The sizes of the AFM probe and
cantilever chip are exaggerated for the purposes of illustration. (b) A representative 2mm
2 mm AFM
image (obtained in air) displaying several pBR322 DNA plasmids deposited onto a mica substrate