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Translocation by
Type I R-M enzymes
Most DNA-based molecular
motors are ‘linear-tracking’ motors and use the repetitive nature of the
repeating nucleotide base-pair to enable them to move along DNA. The best
example, and one of the most closely studied at the single-molecule level,
is RNA polymerase (Harada
et al., 2001). This enzyme is responsible for synthesis of
messenger RNA (the reading intermediate between DNA and protein) and uses
the energy of this synthesis reaction to enable movement along the DNA,
reading the bases as it moves and copying them into a single chain RNA
molecule. Many other motors follow this pattern, but usually have different
functions and as a consequence interact differently with DNA (e.g. DNA
helicases are responsible for unwinding the two strands of DNA, DNA
polymerase synthesises a new strand of DNA, DNA repair enzymes are able to
detect and remove damaged bases in the DNA).
Figure 1
 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).
Figure 2
 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 a collision with another type I R‑M enzyme, or, due
to a 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.
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