With atomic force microscopy (AFM) we systematically studied the DNA condensations on mica surfaces induced by multivalent cation spermidine. The pattern of the DNA condensates is a flat single layer, with a core in the centre and DNA wrapping around it at high density. We assume this to be a two-dimensional condensation of free coiled DNA onto negatively charged mica surfaces by the multivalent cation. The DNA molecules condense on mica surfaces via a pathway different from the formation of toroids, rods or globules in bulk solutions. We give an explanation to why toroid structures are difficult to be observed by AFM, and further discuss the relationship between DNA condensations in solutions and on mica surfaces. The present work will be helpful for understanding the behaviors of DNA on charged surfaces, which might be significantly different from that in solutions.
ZHANG XingHua HOU XiMiao JI Chao LIMing DOU ShuoXing WANG PengYe
During the assembly of many viruses, a powerful molecular motor packages the genome into a preassembled capsid. The Bacillus subtilis phage φ29 is an excellent model system to investigate the DNA packaging mechanism because of its highly efficient in vitro DNA packaging activity and the development of a single-molecule packaging assay. Here we make use of structural and biochemical experimental data to build a physical model of DNA packaging by the φ29 DNA packaging motor. Based on the model, various dynamic behaviours such as the packaging rate, pause frequency and slip frequency under different ATP concentrations, ADP concentrations, external loads as well as capsid fillings are studied by using Monte Carlo simulation. Good agreement is obtained between the simulated and available experimental results. Moreover, we make testable predictions that should guide future experiments related to motor function.
