During DNA synthesis, replication fork progression can be compromised by replication fork barriers (RFBs) which can results from various situations (DNA damage, DNA/protein complexes, DNA secondary structures...). Depending on the nature of the replication block, multiple pathways can be employed to restart fork progression: homologous recombination, template switch and trans-lesion synthesis. Failures in these pathways can results in inability to resume correctly DNA replication and genetic instability. While many factors are involved in the restart or protection of arrested fork, how they help to bypass or correct the causative problem and what are exactly their precise functions at stalled forks is largely unknown. In addition, homologous recombination can also be deleterious during DNA replication and specific pathways are involved in the avoidance of improperly processed recombination intermediates that are toxic for cells. To get insight into the understanding of those mechanisms, we intend to develop methodologies to visualize and to characterize (at both qualitative and quantitative levels) replication and recombination intermediates formed both in vivo and in vitro. To date, it is clear that only physical analyses and sophisticated imaging of replication and recombination intermediates will allow a deeper investigation of their DNA structures. Such interdisciplinary goals can be achieved by joining biological laboratories disposing of elegant model systems with molecular imaging laboratories disposing of powerful techniques allowing deep and precise investigations of physical characteristics of DNA structures. Therefore, we propose to combine molecular biology (such as 2D-gel and DNA combing), and biochemistry with molecular imaging such as electronic microscopy, AFM and fluorescent microscopy. The development of new tools from molecular imaging techniques to study and characterize replication and recombination intermediates at the molecular level is at the heart of this project. Our proposal aims at the emergence of new concepts relative to fundamental biological processes such as DNA replication and recombination and to the development of new methodologies allowing DNA species to be analyzed in a great number of organisms.