Identification of hemicatenane-specific binding proteins by fractionation of Hela nuclei extracts

DNA hemicatenanes (HCs) are DNA structures in which one strand of a double stranded helix passes through the two strands of another double stranded DNA. Frequently mentioned as DNA replication, recombination and repair intermediates, they have been proposed to participate in the spatial organization of chromosomes and in the regulation of gene expression. To explore potential roles of HCs in genome metabolism, proteins capable of binding specifically HCs were purified by fractionating nuclear extracts from Hela cells. This approach identified three RNA-binding proteins: the Tudor-Staphylococcal Nuclease Domain 1 (SND1) protein and two proteins from the Drosophila behavior human splicing family, the ParaSpeckle Protein Component 1 and the Splicing Factor Proline- and Glutamine- rich protein. Since these proteins were partially pure after fractionation, truncated forms of these proteins were expressed in E. coli and purified to near homogeneity. The specificity of their interaction with HCs was re-examined in vitro . The two truncated purified SND1 proteins exhibited a high specificity for HCs, suggesting a role of SND1 protein in targeting the basic transcription machinery to HC structures.