Biology Reference
In-Depth Information
22 ms.
32
However, the likelihood of a UvrA
2
B
2
complex landing
directly on a lesion in DNA has a low probability, and a large number of binding
and dissociation steps would be required to adequately find DNA damage
during a period of cellular division using a 3D searching strategy.
This problem is exacerbated by the presence of a vast excess of undamaged
DNA for which the UvrA
2
B
2
complex has affinity. In reality, however, the
presence of excess nontarget sequences has been shown to accelerate target
acquisition
33
, suggesting that such a 3D searching strategy is an inadequate
explanation.
Alternative mechanisms of target search include DNA sliding or hopping,
which reduces the search space from three dimensions to one. Using techni-
ques described below, researchers have found several proteins to slide various
distances on DNA (see
Table I
). It should be noted, however, that the one-
dimensional (1D) diffusion constants laid out in
Table I
are all slower than
those expected considering the hydrodynamics of motion. The helical structure
of DNA offers a unique challenge to a one-dimensionally diffusing molecule.
Consider by analogy a modern rollercoaster ride, in which there are corkscrew
sections analogous to the helical groove of DNA. The rollercoaster car spins as
it traverses these sections whereas over the linear sections the car slides rapidly
unimpeded by any spiraling. In direct analogy, the drag experienced by a
protein that slides along DNA without being confined to the helical structure
of the DNA is much less than that by a protein corkscrewing around the DNA
along the grooves. Let us first consider the case of a sphere the size of a protein
(r) sliding in one dimension. Ignoring the DNA helix, we calculate the maxi-
mum possible diffusion constant (
bacterium in
r
) and compare this to the mea-
sured value from
Table I
. This difference in diffusion constant provides
information on the magnitude of the energy barrier to diffusion. In all cases,
the value is extraordinarily large. Instead, if we calculate the maximum diffu-
sion constant based on the protein spiraling around the DNA, we find that the
drag due to rotation (effective friction factor
¼k
B
T/6
p
10
9
]
2
)
has a major effect on the diffusion constant,
53
thus lowering the theoretical
maximum value. In turn, this lowers the difference between the expected and
measured diffusion constants and thus the associated energy barrier to reason-
able values ranging from near zero to just a few
]
2
¼
1
þ
4/3[2
p
þ
[
r
/3.4
k
B
T.
Early studies looking at the processivity of UvrABC-mediated repair of
DNA damage in plasmids suggested that the UvrA
2
B
2
complex is capable
of limited 1D DNA scanning. These studies showed that following a lag
period after UV-induced damage, during which plasmids were bound,
UvrA
2
B
2
utilized some type of scanning mechanism to search for and repair
lesions.
29
This study also implied that incision and gap filling were highly
coupled, preserving the topological state of the plasmid with no accumulation
of nicked plasmids.
