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DNA Mismatch Repair

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Nucleotides G, C, A, T

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DNA polymerase

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DNA Mismatch Repair

During DNA replication and recombination, mismatches of bases can occur. These are corrected by DNA mismatch repair (MMR). There are two pathways, one found in eukaryotes and most of the prokaryotes, and the other in E.coli. Both pathways involve identifying sites of mismatch, cutting the DNA segments containing the incorrect bases, and inserting the correct nucleotides. However, the enzymes involved differ.

Causes of mismatches

DNA is a double helix, with each strand made of a sequence of nucleotides. These strands, in turn, consist of deoxyribose sugar, phosphate, and a base. There are two complementary pairs of bases: adenine and thymine, and guanine and cytosine. DNA replication and transfer of hereditary information is based on the complementarity of bases.

  1. DNA Replication

DNA ReplicationDNA replication is semi-conservative, meaning the two daughter DNAs have one strand from the original DNA and a new synthesized strand. During replication, the double helix of the DNA is separated, and polymerase enzymes assemble the new strand by pairing a nucleotide with a base to its complementary pair on the original strand.

Sometimes there are errors in replication, and mismatches occur. Instead of pairing a thymine nucleotide with adenine, for example, a guanine nucleotide is attached. Mismatches occur once in several millions in bases that are assembled to make the new strands.

  1. Heteroduplex recombination

 Mismatches can also occur during meiosis, when DNA from non-sister chromatids of a pair of homologous chromosomes are exchanged during crossing-over. The neighboring strands are broken at the same point in both chromosomes, and the strand crosses over to join with the other chromosome. The length of the strands that are exchanged can vary. When small parts are exchanged, the homologous pair has short heteroduplex regions. When the whole ends of chromatids are exchanged, recombined DNA is formed. In both cases, many mismatched pairs of bases result. Mismatch repair also ensures that only the homologous sequences are exchanged.

  1. DNA damage

DNA damage can happen for many reasons in both prokaryotes and eukaryotes.

DNA Mismatch Repair

 If left uncorrected, DNA mismatches can lead to mutations in somatic or germline cells genes. Therefore, DNA mismatch repair (MMR) is critical to maintaining genetic stability. The steps involved in MMR are as follows:

  1. Recognition of mismatch and strand discrimination
  2. Excision of mismatches
  3. Synthesizing the correct nucleotides 
  1. Recognition of mismatch and strand discrimination

Recognition of mismatches involves different sets of proteins in the two pathways which bind themselves to the mismatch. The sites of mismatch are not smooth, but are irregular, and therefore don't bond well. Recognition is carried out by MutS in E.coli, and in eukaryotic MMR by Msh2/Msh6 (MutSα) and Msh2/Msh3 (MutSβ).

 These proteins then slide along the DNA in both directions to determine which of the strands is the newly synthesized one. This is so only the incorrect nucleotides from the newly synthesized strands are replaced and the original sequence of nucleotides remains intact. The process is important to maintain genetic integrity.

 In eukaryotic MMR, strand discrimination is based on finding discontinuities or nicks found in the newly synthesized strands.

 In E. coli, MMR  involves recognizing absence of methylation. Methyl groups are not immediately added to DNA on formation, but require time. Only the original DNA strand has methyl groups, attached to the base adenine.

  1. Excision of mismatches

 In eukaryotic MMR, once the nick on the new strand is found, the MutSα and MutSβ attract an enzyme called Exonuclease (Exo 1) or (Exo3, in the case of humans). Exonuclease then removes all the nucleotides starting from the nick and travelling in a 5' to 3' direction, including the incorrect base and a few correct bases. In all, several hundred nucleotides can be removed or excised.

In E. coli MMR, MutH and MutL cut the un-methylated daughter DNA strand that has the mismatch, and excision of the discarded section is performed by Exonuclease (ExoI, ExoVII, ExoX, RecJ or SSB).

  1. Synthesizing the correct nucleotides

In eukaryotic MMR, there is a complex of other enzymes also involved during the excision (MutS, MutL, RPA, PCNA, RFC). These enzymes are also necessary to stimulate polymerase delta, which synthesizes and strings along the new complementary nucleotides. Finally, the enzyme Ligase binds the DNA strand together. In E. coli MMR the synthesis is performed by DNA polymerase III and Ligase.


In human DNA, 130 genes are involved in MMR. Without MMR, or in case of defects in MMR, the rate of spontaneous mutation increases, and these mutations can lead to nonpolyposis colon cancers, sporadic tumors, and resistance to certain chemotherapeutic agents in humans, and also abnormalities in meiosis and sterility in mammalian systems.

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