Credit: © 2008 AAAS

DNA replication involves a process where a polymeric thread of single-stranded DNA is moved through a pore in the protein DNA-polymerase. A similar process occurs when a protein moves through a pore in a cell membrane. However, the mechanism of this threading is not well understood. Now, Alan Rowan, Roland Noelte and co-workers from the Radboud University of Nijmegen, Netherlands, and the Università di Roma Tor Vergata, Italy, have studied1 a model system that provides a deeper understanding of the process.

The model consists of a macrocycle, through which a polymer chain is threaded, with both moieties incorporating complementary binding units. A large blocking group is placed at one end of the polymer thread, next to its binding unit. For binding to occur, the free end of the polymer must be threaded through the macrocycle, which must then 'hop' along the thread until it reaches the binding unit. The polymer binding unit is fluorescent when unbound, and fluorescence quenching occurs only when the entire polymer has been threaded through the macrocycle. To investigate the threading process, Rowan and co-workers studied the influence of polymer chain-length on the rate of fluorescence quenching.

It was shown that before threading, an interaction between the chain and the outside of the macrocycle is important for all but the shortest chains — the polymer chain then loops around to thread through the macrocycle. A similar assisted threading mechanism is very likely to operate in natural systems.