Plasmid DNA imaged by Atomic Force Microscopy

Radiation induced DNA fragment distribution seems to be missing information crucial for understanding of biological impacts of DNA clustered damages. First, the produced DNA fragments may interfere within pathways involved in repair of the clustered damages. Second, measurements of the clustered damages by conventional techniques are negatively affected by limits in fragments' detection. Therefore, our project is aimed to characterization of radiation induced DNA fragment-length distribution by use of atomic force microscopy (AFM). In this contribution we introduce preliminary tests performed in laboratories of ESTEC (European space research and technology center). Several substrates for DNA plasmid AFM imaging were tested (glass, silicon wafer and mica), as well as fixing methods. The DNA on the substrates was imaged in the air with AFM in tapping mode; we will discuss optimal cantilever and scanning parameters. The AFM images have been started to analyze in order to a) distinguish plasmid forms of different conformation (supercoiled, circular, and linear) according to a level of plasmid DNA damage, since this information can be compared to conventional techniques such as electrophoresis; b) measure lengths of the linear forms. (authors)