DNA Repair

DNA bases that have been modified by the addition or loss of a small chemical group as described above are repaired by the BER pathway (Figure 3). The BER pathway begins with the excision of a damaged base by an enzyme called DNA glycosylase (Figure 3, step 1). DNA glycosylases bind to chemically altered (damaged) bases and catalyze the cleavage (hydrolysis) of the Figure 3. Schematic diagram of the base excision repair pathway. The damaged base (in this case, guanine) is removed by a glycosylase enzyme. This creates an AP-site, which is recognized and cleaved by AP-endonuclease. DNA polymerase fills in the gap. DNA ligase links the broken strand together again. bond linking the modified base to its sugar, which results in the release of the modified base from the DNA chain and in the insertion of an AP-site. Several types of DNA glycosylases exist, each one specifically excising a different type of damaged base. It is important that a DNA glycosylase act only on damaged and not natural DNA bases, otherwise too many baseless sugars would be produced, weakening the integrity of the DNA chain.

Excision of the damaged base by a DNA glycosylase creates an AP-site, which in turn is acted upon by the second enzyme in the BER pathway, apurinic/apyrimidinic (AP) endonuclease (Figure 3, step 2). The most abundant AP-endonuclease in human cells cleaves (incises) the sugar-phosphate backbone on the left side of the baseless sugar to yield a one-nucleotide gap. On the left margin of the incision is a normal nucleotide (DNA base + sugar + phosphate); however, the right margin of the gap contains the baseless sugar-phosphate residue.

In order to fill the gap (replace the missing nucleotide), an enzyme specialized in synthesizing DNA, a DNA polymerase, will insert the correct nucleotide into the gap and link it to the normal nucleotide on the left margin by recognizing which base is opposite the gap on the complementary DNA strand. Figure 3, step 3 shows that the DNA polymerase recognizes that a G nucleotide is needed since the complementary base is a C. Note that an entire nucleotide is added here, not just a base. Before DNA polymerase is finished with the repair of the one-nucleotide gap, it removes the baseless sugar phosphate left behind by AP-endonuclease.

At this point, repair of the gap is almost, but not quite, finished, since there is a "nick" in the top DNA strand at the right margin of the former gap. Thus, the final step in the BER pathway is to ligate the DNA strands on both sides of the nick (Figure 3, step 4). If we examine the sugar phosphate DNA chain shown in Figure 2, we can see that the sugars that carry the DNA bases are linked together by phosphate groups. This type of linkage is referred to as a phosphodiester bond. The enzyme DNA ligase joins the strands by creating a phosphodiester bond between them, sealing the nick. In summary, the basic steps of the BER pathway are damage recognition and base excision, AP-site incision, DNA repair synthesis, and DNA ligation.