Electron-microscopic localization of the binding of Escherichia coli RNA polymease to T7 DNA in vitro

Quantitative electron microscopic analysis of DNA-protein interactions

Electron microscopy offers a unique potentiality to visualize individual molecules. For the last 30 years it has been used to study the structure and the interactions of various biological macromolecules. The contribution of electron microscopy is important because of its capacity to demonstrate the existence of conformational structures such as kinks, bents, loops, etc., either on naked DNA, or on DNA associated with various proteins or ligands. Increasing interest was given to such observations when it was found that they provide a direct visualization of interacting molecules involved in DNA metabolism and gene regulation. Technical advances in the preparation of the specimens, their observation in the electron microscope, and the image processing by computers have allowed the shifting from qualitative to quantitative analysis, as illustrated by a few examples from our laboratory.

Adhesion of particulate specimens to support films for electron microscopy: a model system for assessing the surface properties of support films, and its application to chromatin particles

Silica microspheres bearing a known surface charge were used to test the adhesive properties of support films and support film treatments commonly used in the electron microscopy of particulate specimens. Adhesion was strongly correlated with surface charge, negatively charged microspheres binding well only to positively charged support films and vice versa in solutions of low ionic strength. This charge dependency could be overcome by increasing the ionic strength to about 100 mmol with monovalent cations; under these conditions, it was not necessary to provide an oppositely charged film surface to obtain adhesion. Chromatin particles (nucleosomes) which have a net negative charge, behaved very much like the negatively charged silica with respect to adhesion, confirming that the microspheres provided an accurate indication of support film surface properties. The chromatin particles showed dramatic structural changes under conditions when adhesion was either poor, or very strong, indicating the need for careful selection of binding conditions for delicate biological specimens. A new and simple method for pretreating carbon films to improve adhesion was developed, and a preliminary account of this technique is presented.

DNA electron microscopy

In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).

Adsorption of DNA molecules to different support films

Protein-free adsorption of the DNA of the Escherichia coli bacteriophage T7 to carbon, collodion, aluminium-beryllium and aluminium films was studied. It was found that the appearance of DNA strands depended greatly upon the kind of support film used. Direct adsorption of DNA to aluminium-beryllium or aluminium films yielded specimens with 'thin and long' and 'thick and short' regions along the strand. Well extended, uncoiled and unaggregated DNA molecules were obtained only when DNA was adsorbed to carbon, collodion or mica in the presence of intercalating dyes such as ethidium bromide. Adsorption properties of the different films are well correlated with their surface charge. Aluminium-beryllium films carry a strong positive surface charge, aluminium films a weak positive charge and carbon films a weak negative charge. It is suggested that for the preparation of specimens by spontaneous adsorption of well extended and unaggregated strands it is necessary that the DNA molecule is stiffened by a ligand such as an intercalating dye, and that the charge on the surface of the support film is opposite to the charge of the macromolecule.