The maintenance of genomic integrity in the form of the organism-specific nucleotide sequence of the genome is essential for preservation of the species during propagation. This requires an extremely high fidelity of DNA replication. Errors in RNA synthesis may be tolerated at a significantly higher level because RNAs have a limited half-life, even in nondividing cells, and are redundant. In contrast, any error in DNA sequence is perpetuated in the future, as there is only one or two copies of the genome per cell under most circumstances. Obviously, all organisms have a finite rate of mutation, which may be necessary for evolution. Genetic errors are one likely cause of such mutations. Inactivation of a vital protein function by mutation of its coding sequence will cause cell death. However, mutations that affect nonessential functions could be tolerated. Some of these mutations can still lead to change in the phenotype, which in extreme cases can cause pathological effects. In other cases, these may be responsible for susceptibility to diseases. In many cases, however, such mutations appear to be innocuous and are defined as an allelic polymorphism. The mammalian genome appears to have polymorphism in one out of several hundred base pairs. Such mutations obviously arose during the evolution and subsequent species propagation.
about 10−6 to 10−7 per incorporated deoxynucleotide. The catalytic units of the replication machinery, namely, DNA polymerases, have a significantly higher error rate of the order of 10−4 to 10−5 per deoxynucleotide. In fact, some DNA polymerases, notably the reverse transcriptases of retroviruses, including HIV, the etiologic agent for AIDS, are highly error prone and incorporate a wrong nucleotide for every 102–103 nucleotides. These mistakes result in a high frequency of mutation in the viral protein, which helps the virus escape from immunosurveillance. The overall fidelity of DNA replication is significantly enhanced by several additional means. The editing or proof-reading function of the replication machinery is a 3´→5´ exonuclease (which is either an intrinsic activity of the core DNA polymerase or is present in another subunit protein of the replication complex) which tests for base pair mismatch during DNA replication and removes the misincorporated base. Such an editing function is also present during RNA synthesis. In addition, after replication is completed, the nascent duplex is scanned for the presence of mispaired bases. Once such mispairs are marked by mismatch recognition proteins, a complex mismatch repair process is initiated, which causes removal of a stretch of the newly synthesized strand spanning the mismatch, followed by resynthesis of the segment, as described later.
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