Atomic force microscopy of uncoated plasmid DNA: nanometer resolution with only nanogram amounts of sample

Application of the molecular combing technique to starch granules

The molecular combing technique was used to dissociate the nanostructural units of starch granules from the starch fragments after a gelatinization process. With the help of atomic force microscopy (AFM), we observed that some nanostructural chains were just flowing out of the granules. It proves that there are substantive nanostructural units in the starch granules, a phenomenon not previously observed, so these nanostructural units were defined as suspected intermediates. Furthermore, we conclude that blocklets of starch granules are formed through twisting or distortion of nanochains.

Oligomeric interaction of the PapB transcriptional regulator with the upstream activating region of pili adhesin gene promoters in Escherichia coli

Transcriptional regulation of the pap genes, which encode fimbrial adhesins in uropathogenic Escherichia coli, depends on an upstream activating region. This region contains binding sites for a transcription factor, PapB, which is a member of a growing family of putative regulatory proteins found in several virulence-associated fimbrial gene systems. To assess the nature of the PapB binding sites, we studied different naturally occurring variants and a number of in vitro constructed mutant binding sites. DNase I footprinting analysis and visualization of the PapB-DNA complex by atomic force microscopy showed that the protein occupied a DNA region of more than 50 bp. Purified PapB protein was shown to recognize a motif including a 9 bp repeat sequence containing T/A triplets at a conserved position. PapB binding was affected by distamycin, and the results were consistent with the possibility that the binding to DNA occurred through minor groove interaction. From these analyses and estimation of the relative number of PapB proteins per binding site, we suggest that PapB binds the DNA in an oligomeric fashion and may function as an architectural factor in the transcriptional control of adhesin expression.

Imaging polysaccharides by atomic force microscopy

Techniques have been developed for the routine reliable imaging of polysaccharides by atomic force microscopy (AFM). The polysaccharides are deposited from aqueous solution onto the surface of freshly cleaved mica, air dried, and then imaged under alcohols. The rationale behind the development of the methodology is described and data is presented for the bacterial polysaccharides xanthan, acetan, and the plant polysaccharides l-carrageenan and pectin. Studies on uncoated polysaccharides have demonstrated the improved resolution achievable when compared to more traditional metal-coated samples or replicas. For acetan the present methodology has permitted imaging of the helical structure. Finally, in addition to data obtained on individual polysaccharides, AFM images have also been obtained of the network structures formed by kappa-carrageenan and gellan gum.

Scanning probe microscopy in microbiology

Scanning probe microscopy (SPM) is emerging as an important alternative to electron microscopy as a technique for analyzing submicron details on biological surfaces. Microbiological specimens such as viruses, bacteriophages, and ordered bacterial surface layers and membranes have played an important role in the development of scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) in cellular and molecular biology. Early STM studies involving metal-coated bacteriophage T4 polyheads, Methanospirillum hungatei, and Deinococcus radiodurans HPI layer clearly demonstrated that resolution was comparable to TEM on similarly prepared specimens and only limited by metal graininess. However, except for thin films or layers, novel biological information has been difficult to obtain since imaging native surfaces of such biomaterials as proteins or nucleic acids by STM proved to be unreliable. With the development of atomic force microscopes, which allow imaging of similar native structures, SPM applications have widened to include straightforward surface structure analysis, analysis of surface elastic and inelastic properties, bonding force measurements between molecules, and micro-manipulations of such individual molecules as DNA. AFM images have progressed from relatively crude representations of specimen topography to nanometer scale representations of native hydrated surfaces. It appears from the study of microbiological specimens that direct visualization of dynamic molecular events or processes may soon become a reality.

Observation of the helical structure of the bacterial polysaccharide acetan by atomic force microscopy

A method has been developed that has been found to give reproducible images of uncoated polysaccharides by Atomic Force Microscopy (AFM). Aqueous solutions of the polysaccharide are deposited as drops onto freshly cleaved mica surfaces, air dried, and then imaged under butanol. The method has been used to obtain images of the bacterial polysaccharide acetan. In regions within the deposited sample, where the molecules are aligned side-by-side, it has been possible to observe a periodic structure along the polysaccharide chain, attributable to the helical structure of acetan.

The scanning force microscopy of DNA in air and in n-propanol using new spreading agents

We present recent advances in DNA specimen preparation technique for scanning force microscopy (SFM) based on spreading on mica in the presence of cationic and non-ionic detergents. Reproducible DNA imaging in air and in n-propanol has been achieved in the presence of the non-ionic detergent 2,4,6-tris(dimethylaminomethyl) phenol (DMP-30) or the cationic detergent cetylpyridinium chloride (CP) in a microdrop containing nanograms of DNA. In an alternative procedure, a microdrop of detergent is applied to the surface just prior to the DNA. Quantitative image analysis yields as the apparent molecular dimensions of the DNA a width of approximately 7 nm and a height of approximately 0.7 nm, and delineates the problems of DNA metrology by SFM.

Scanning force microscopy of circular and linear plasmid DNA spread on mica with a quaternary ammonium salt

Scanning force microscopy (SFM) offers the potential for subnanometer resolution in the investigation of nucleic acids, proteins, and their complexes. SFM is not bound by the requirement of classical transmission electron microscopy (TEM) for contrast enhancement through shadow casting or negative staining. A primary challenge, however, has been the reproducible fixation of samples on an atomically flat surface such as mica. We have developed a method for the routine imaging by SFM of supercoiled, relaxed, and linearized plasmid DNA, immobilized on freshly cleaved mica through the spreading action of benzyldimethylalkylammonium chloride (BAC) at micromolar concentrations. A reproducibly high yield of well-spread, dispersed molecules is obtained and background contamination is minimal. The contour lengths of the relaxed and linearized molecules imaged in air agree well with the helical rise (3.4 A/bp) of B-DNA in solution. We have also introduced the use of quantitative image analysis of SFM images to determine apparent molecular width and height over the entire molecular path.

Recent advances in atomic force microscopy of DNA

Three advances involving DNA in atomic force microscopy (AFM) are reported here. First a HEPES-Mg buffer has been used that improves the spreading of DNA and provides good DNA coverage with as little as 200-500 picograms per sample. Second, the new "tapping" mode has been used to improve the ease and resolution of AFM-imaging of DNA in air. Finally, AFM images are presented of single-stranded phi X-174 virion DNA with the gene 32 single-stranded binding protein. A summary of the current state of the field and of the methods for preparing and imaging DNA in the AFM is also presented.