Relationships between the winding angle, the characteristic radius, and the torque for a long polymer chain wound around a cylinder: implications for RNA winding around DNA during transcription

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. We propose a model for co-transcriptional R-loop formation, in which their generation requires passage of the nascent RNA "tail" through the gap between the separated DNA strands. This passage becomes increasingly difficult with lengthening of the RNA tail. The length of the tail increases upon increasing distance between the transcription start site and the site of R-loop initiation. This causes reduced yields of R-loops with greater distance from the transcription start site. However, alternative pathways for R-loop formation are possible, involving either transient disruption of the transcription complex or the hypothetical formation of a triple-stranded structure, as a "collapsed R-loop." These alternative pathways could account for the fact that in many systems R-loops are observed very far from the transcription start site. Our model is consistent with experimental data and makes general predictions about the kinetics of R-loop formation.

R-loop generation during transcription: Formation, processing and cellular outcomes

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 strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders. We provide a perspective on mechanistic aspects of R-loop formation and their resolution learned from studies in model systems. This should contribute to improved understanding of R-loop biological functions and enable their practical applications. We propose the novel employment of artificially-generated stable R-loops to selectively inactivate tumor cells.

Torque-winding interdependence for a flexible polymer chain wound around a cylinder in the presence of obstacles

Polymer chains winding around each other or around other objects occur in many natural systems; the physical consequences of this winding are therefore of significant interest. A polymer chain could be surrounded by various bulky objects (referred as obstacles), such as other macromolecules or macromolecular aggregates. Here we show that for a long flexible polymer chain wound around a cylinder, the presence of obstacles could modify the winding-torque interdependence, in some cases leading to phase-transition-like behavior in which the winding occurs only when the torque exceeds some critical value. Possible implications of this effect are discussed in relation to the biophysics of nucleic acids.