Biology Reference
In-Depth Information
It is valid to assume that the distance a protein could slide before encoun-
tering another protein bound to DNA is very short given the large numbers of
DNA-binding proteins. Thus, an alternative to DNA sliding has been proposed,
DNA hopping, in which the protein performs microdissociation and reassocia-
tion without undergoing macro-dissociation away from the DNA helix (see
Fig. 2
). This interaction is thought to be mediated by an ionic interaction
between the protein and DNA; most DNA-binding proteins possess a positively
charged DNA-binding cleft such as that found at the dimer interface of UvrA.
2
In order to discriminate between sliding and hopping, researchers use buffers
containing different ionic strengths.
54
The rate of sliding is believed to be
independent of ionic strength in a purely ionic-mediated system because there
is no change in the number of ions bound as the proteins move. However,
hopping is greatly affected by the ionic strength as the ionic-mediated association
of the protein to the DNA will be shielded with increasing salt concentrations,
leading to shorter attached lifetimes and potentially more rapid diffusion.
55
One
extreme form of hopping is jumping, in which the UvrA
2
B
2
complex could
rebind to a second DNA helix at a great sequence distance from the initial
DNA-binding site. This could occur inside a living cell where the local DNA
concentration is very high. However, regardless of the two types (sliding or
hopping) of movement on DNA, with no input of external energy, the probability
of stepping in one direction versus the other is equal and therefore there is no net
Hopping
Jumping
Sliding
3D searching
Directed motion
Intersegmental transfer
Combination of 3D and
1D search
F
IG
. 2. Potential modes of DNA damage searching by UvrA and UvrAB repair proteins.
A number of mechanisms by which proteins can search for lesions are depicted. Hopping is
distinguished from jumping by the distance over which the translocation occurs; however, in both
cases, the protein remains within close proximity of the DNA. Sliding suggests that the protein
remains in constant contact with the DNA, making it difficult to separate from hopping. If the
protein dissociates from DNA into bulk solution, then a 3D search is employed to find the target
site. Directed motion requires the input of energy in the form of nucleotide.
