A model for transcription-dependent R-loop formation at double-stranded DNA breaks: Implications for their detection and biological effects.

R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. During R-loop formation an RNA strand invades the DNA duplex, displacing the homologous DNA strand and binding the complementary DNA strand. Here we analyze a model for transcription-dependent R-loop formation at double-stranded DNA breaks (DSBs).

Topology and kinetics of R-loop formation.

R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. They can be formed upon "invasion" of an RNA strand into a DNA duplex, during which the RNA displaces the homologous DNA strand and binds the complementary strand. R-loops have many significant beneficial or deleterious biological effects, so it is important to understand the mechanisms for their generation and processing.

Effects of isolated nonspecific binders upon the search for specific targets: Absolute rates versus competition between the targets.

Many biological processes involve macromolecules searching for their specific targets that are surrounded by other objects, and binding to these objects affects the target search. Acceleration of the target search by nonspecific binders was observed experimentally and analyzed theoretically, for example, for DNA-binding proteins. According to existing theories this acceleration requires continuous transfer between the nonspecific binders and the specific target.

Transcription Inhibition by PNA-Induced R-Loops.

R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template DNA strand. R-loops occur naturally in all kingdoms of life, and they have multiple biological effects.