  The insertion of HIV and other DNA elements within genomes underpins both
genetic diversity and disease when unregulated. Most of these insertions are
not random and occupy specific positions within the genome but the physical
mechanisms underlying the integration site selection are poorly understood.
Here we perform Molecular Dynamics simulations to study the insertion of DNA
elements, such as HIV viral DNA or transposons, into naked DNA or chromatin
substrate. More specifically, we explore the role of loops in the DNA substrate
and discover that they act as "geometric catalysts" for DNA integration.
Additionally, we discover that the 1D and 3D clustering of loops affects the
distribution of integration sites. Finally, we show that loops may compete with
nucleosomes at attracting DNA integrations. These results may be tested in
vitro and they may help to understand patterns of DNA insertions with
implications in genome evolution and gene therapy.
