AFM visualization of protein-DNA interactions

Proteins are the principal mediators of DNA processes and organization. Enzymes and regulatory proteins perform cellular processes, such as replication, transcription, and recombination; while architectural proteins are involved in the organization of DNA within the cell into structures, such as chromatin. DNA is a long polymeric molecule, ranging in size of several thousand monomeric units (bacteriophage genome) to a million base pairs (eukaryotic genome); therefore, nanoscale imaging tools are instrumental in understanding the mechanisms of genetic processes and intracellular DNA organization. Historically, electron microscopy (EM) was widely employed to study the various properties of DNA. Of particular note, EM imaging was critical in proving the nucleosomal organization of DNA within the cell by graphically illustrating the beads-on-a-string model of unfolded chromatin and elucidating the higher order structure of chromatin [see Watson (2008) and numerous references therein]. The advent of atomic force microscopy (AFM), and the application of this nanoimaging technique to molecular biology, opens new prospects for studies of protein-DNA complexes. AFM technology allows for a gentle sample preparation, easing concerns about sample preservation. Moreover, AFM is capable of imaging samples in fully hydrated states by scanning in aqueous solutions. Therefore, in addition to nanoscale static structural data of protein-DNA complexes, AFM visualizes the dynamics of conformational transitions of DNA and various nucleoprotein complexes.