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chapter 24

DNA Replication, Repair, and Mutagenesis

Excision and

gap filling

Ligation

Ligafion

Breakage of N-glycosidic bond of

n cisio n

T dimer and cleavage 3' lo uncut T

Displacement by polymerase

FIGURE 24-15

Two modes of excision repair, (a)

Escherichia coli

mechanism. Two incision steps are followed by gap-filling and

displacement by polymerase I. (b)

Micrococcus luteus

mechanism. A pyrimidine dimer glycosylase breaks an

N-glycosidic bond and makes a single incision. Pol I displaces the strand, which is removed by an exonucleolytic event.

In both mechanisms, the final step is ligation.

in

E. coli,

pol I polymerizes from this end and displaces

the dimer-containing strand. After the dimer has been dis-

placed, a second cut is made, the displaced strand falls

away, and ligase forms the final phosphodiester bond. Re-

pair of dimers in mammalian cells is more complicated

and poorly understood, and requires a larger collection of

enzymes.

Recombination Repair

Recombination repair is a mechanism for generating a

functional DNA molecule from two damaged molecules.

It is an essential repair process for dividing cells because

a replication fork may arrive at a damaged site, such as

a thymine dimer, before the excision repair system has

eliminated damage.

When pol III reaches a thymine dimer, an adenine is

added to the growing strand. However, the distortion of the

helix caused by the dimer weakens the hydrogen bond and

activates the polymerase editing function, and the adenine

is removed. The cycle begins again—an adenine is added

and then removed—the net result of which is that the repli-

cation fork fails to advance. A cell in which DNA synthesis

is permanently stalled cannot complete a round of repli-

cation and does not divide. However, in a way that is not

understood, after a pause of ~5 seconds per dimer, chain

growth begins again beyond the thymine dimer block. The

result of this process is that the daughter strands have large

gaps, one for each unexcised thymine dimer. Viable daugh-

ter cells cannot be produced by continued replication alone

because the strands having the thymine dimer will con-

tinue to turn out defective daughter strands and the first

set of daughter strands would be fragmented when the

growing fork enters a gap. However, by a recombination

mechanism called

sister-strand exchange

proper double-

stranded molecules can be made.

The essence of sister-strand exchange is that a single-

stranded segment free of any defects is excised from an

undamaged strand on the homologous DNA segment at

the replication fork and somehow inserted into the gap