Single molecule studies of RNA polymerase (and other polymerases) have involved immobilisation of the motor (enzyme) onto a surface; the enzyme will then bind the DNA, which carries a bead at one end (Schafer et al., 1991) . This stage is then followed by measurement of the forces exerted on the bead, required to stall movement along the DNA, by means of an optical trap (effectively a laser light that ‘holds’ the bead at its point of focus).

However, there is another type of DNA-based molecular motor that interacts with a specific site on the DNA and then moves the remaining DNA toward that site. These motors belong to a large superfamily (SF-II) of helicase-like enzymes (Flaus and Owen-Hughes, 2001) and are particularly well illustrated by Type I restriction-modification (R-M) enzymes, but also include type III R-M enzymes, chromatin remodelling factors and a few chimeric enzymes. Type I R-M enzymes are distinguished from other restriction enzymes by the fact that binding to an unmethylated recognition site on the DNA, elicits DNA cleavage at a distantly located, non-specific site on the same DNA molecule. ATP, which is required for DNA restriction, fuels translocation of the distal DNA toward the recognition site (Figure 1). Cleavage occurs when translocation is blocked (Figure 2 and Janscak et al., 1999b) , which can be due to collision with another type I R-M enzyme, or due to lack of DNA to translocate (e.g. on circular DNA Szczelkun et al., 1996) . Rotation is also an inevitable outcome of this translocation as the regular binding surfaces on the DNA are arrayed helically and the translocating motor follows the helical groove.
Figure 1
The solid block represents the recognition
sequence for the enzyme. The enzyme binds
at this site and upon addition of ATP DNA
translocation begins. During translocation,
an expanding loop is produced.


These enzymes are unusual in that they are simple actuators – they move one part of the DNA relative to another section of the DNA and do not require immobilisation on a surface to reproduce measurable motion (although the DNA needs to be surface attached for an observable displacement of a bead). This suggests a simple mechanism for detecting DNA movement through the use of a magnetic bead. In the case of type I R-M enzymes cleavage must be prevented in order to provide a useful molecular motor.

Figure 2
A) The open box is the DNA binding site
for the motor. (B) The wild-type enzyme
has two motor subunits that translocate
the adjacent DNA in a bi-directional fashion.
(C) The hatched block represents a
blockage attached to the DNA.
Collision between the motor and the
blockage results in DNA cleavage.