Jqp

Cut Cut

UvrC cuts on 5' side

UvrB cuts on 3' side

New DNA

'"^S.^Polymerase

New DNA

'"^S.^Polymerase

Polymerase I makes new DNA and degrades displaced strand

UvrD unwinds DNA

Bases that do not occur naturally are removed from DNA by a variety of specific repair systems.

FIGURE 14.17 Removal of Unnatural Bases

An altered base (such as hypoxanthine) is removed by DNA glycosylase leaving an empty, AP site. The AP site is recognized by AP endonuclease, which nicks at the 5' side of the sugar backbone. This leaves a free 3'-OH on the base pair just upstream (above) the AP site. Poll recognizes the 3'-OH and replaces a stretch of single-stranded DNA that includes the AP site.

AP Endonuclease nicks backbone on 5' side 5'

AP Endonuclease nicks backbone on 5' side 5'

FIGURE 14.17 Removal of Unnatural Bases

An altered base (such as hypoxanthine) is removed by DNA glycosylase leaving an empty, AP site. The AP site is recognized by AP endonuclease, which nicks at the 5' side of the sugar backbone. This leaves a free 3'-OH on the base pair just upstream (above) the AP site. Poll recognizes the 3'-OH and replaces a stretch of single-stranded DNA that includes the AP site.

the DNA backbone. Specific DNA glycosylases exist for each unnatural base. Thus uracil-N-glycosylase, Ung protein, removes uracil from DNA. Some methylated derivatives, such as 3-methyl adenine and 3-methyl guanine are removed in the same manner.

Removal of bases leaves an empty space in the DNA known as an AP-site. AP stands either for apurinic or apyrimidinic depending on which type of base was removed to create the AP-site (Fig. 14.17). Next an AP endonuclease cuts the backbone of the DNA next to the missing base leaving a free 3'-OH group. DNA polymerase I then makes a short new piece of DNA starting with the free 3'-OH group. As Poll moves along it degrades the single strand in front of it by its 5'-exonuclease activity. As usual, the final nick is sealed by DNA ligase.

Some unnatural bases are the result of oxidation. 8-Oxoguanine is especially prevalent and will sometimes mispair with adenine leading to an 8oxoG-A base pair (see Ch. 13) instead of a G-C base pair. A specific DNA glycosylase, the MutM protein, removes 8-oxoguanine from DNA. In addition, the MutY protein removes adenine when (and only when) it is found opposite 8-oxoguanine (Fig. 14.18). In both cases removal generates an AP-site that is processed as described above. Finally, 8-oxogua-nine may arise in the nucleotide pool used to synthesize DNA. To repair the defective nucleotides, the MutT protein finds the 8-oxoguanine derivative of GTP and cleaves off two phosphate groups. This prevents the incorporation of pre-formed 8-oxogua-nine into DNA.

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