Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

280 Chapter 5: DNA Replication, Repair, and Recombination
RecA
protein
single-strand DNA in
RecA-bound form
heteroduplex DNA in
RecA-bound form
+
in a way that stretches the duplex, destabilizing it and making it easy to pull the
strands apart. The invading single strand then can sample the sequence of the
duplex by conventional base-pairing. This sampling occurs in triplet nucleotide
blocks: if a triplet match is found, the adjacent triplet is sampled, and so on. In
this way, mismatches quickly lead to dissociation and only an extended stretch of
MBoC6 n5.200/5.50
base-pairing (at least 15 nucleotides) stabilizes the invading strand and leads to
strand exchange.
RecA hydrolyzes ATP, and the steps described above require that each RecA
monomer along the filament be in the ATP-bound state. However, the searching
itself does not require ATP hydrolysis; instead, the process occurs by simple
molecular collision, allowing many potential sequences to be rapidly sampled.
Once the strand-exchange reaction is completed, however, ATP hydrolysis is necessary
to disassemble RecA from the complex of DNA molecules. At this point,
repair DNA polymerases and DNA ligase can complete the repair process, as
shown in Figure 5–48.
ATP
ADP
+
P i
DNA duplex
DNA heteroduplex
Figure 5–49 Strand invasion catalyzed
by the RecA protein. Our understanding
of this reaction is based in part on
structures determined by x-ray diffraction
studies of RecA bound to single- and
double-strand DNA. These DNA structures
(shown without the RecA protein) are
on the left side of the diagram. Starting
at the top, ATP-bound RecA associates
with single-strand DNA, holding it in an
elongated form where groups of three
bases are separated from each other by
a stretched and twisted backbone. In the
next step, the RecA-bound single strand
then binds to duplex DNA, destabilizing it
and allowing the single strand to sample
its sequence through base-pairing, three
bases at a time. If no match is found, the
RecA-bound single strand of DNA rapidly
dissociates and begins a new search. If
an extensive match is found, the structure
is disassembled through ATP hydrolysis,
resulting in the dissociation of RecA
and the exchange of one single strand
of DNA for another, thereby forming a
heteroduplex. (PDB code: 3CMX.)
Homologous Recombination Can Rescue Broken DNA Replication
Forks
Although accurately repairing double-strand breaks, which can arise from radiation
or chemical reactions, is a crucial function of homologous recombination,
perhaps its most important role is in rescuing stalled or broken DNA replication
forks. Many types of events can cause a replication fork to break, and here we consider
just one example: a single-strand nick or gap in the parental DNA helix just
ahead of a replication fork. When the fork reaches this lesion, it falls apart—resulting
in one broken and one intact daughter chromosome. The broken fork can be
flawlessly repaired (Figure 5–50) using the same basic homologous recombination
reactions we discussed above for the repair of double-strand breaks. With
slight modifications, the set of reactions depicted in Figures 5–48 and 5–50—
known collectively as homologous recombination—can accurately repair many
different types of DNA damage.
Cells Carefully Regulate the Use of Homologous Recombination in
DNA Repair
Although homologous recombination neatly solves the problem of accurately
repairing double-strand breaks and other types of DNA damage, it does present