Replication fidelity rates

DNA replication under low-fidelity conditions, typically error-prone PCR (Arkin, 1992 Zaccolo, 1999) the method is simple and convenient, but the conservative nature of the genetic code limits the available substitutions to only five to seven amino acid substitutions per codon and the incorporation of stop codons limits the acceptable mutation rate to around two amino acid substitutions per gene (Smith, 1993 Arnold, 2000) ... 

A major goal of directed evolution of DNA polymerases has been to elucidate the structural elements that confer high fidelity during DNA replication. If DNA polymerases were to rely solely on the stability of nucleotides that aligned with template for discrimination of correct template-directed polymerization, the error frequency would be in the order of one mispaired nucleotide per 100 incorporated [23], The measured error rate for incorporation and extension of a mismatched nucleotide attributable to DNA polymerases lacking an error correcting exonucleolytic activity range... 

Except for the altered forms of T7 DNA polymerase and Taq DNA polymerase (23), all of the DNA polymerases identified above contain a 3 - 5 exonuclease function that specifically degrades single-stranded DNA to produce 5 -nucleo-side monophosphates. In vivo, the 3 - 5 exonuclease functions during DNA synthesis to hydrolyze misincorpo rated nucleotides at the 3 -terminus of a growing DNA chain, and in doing so contributes as much as a factor of 100 to the overall fidelity of DNA replication (24, 25). 

It is noteworthy that RNA polymerase lacks nuclease activity. Thus, in contrast with DNA polymerase, RNA polymerase does not correct the nascent polynucleotide chain. Consequently, the fidelity of transcription is much lower than that of replication. The error rate of RNA synthesis is of the order of one mistake per 10 or lO nucleotides, about 10 times as high as that of DNA synthesis. The much lower fidelity of RNA synthesis can be tolerated because mistakes are not transmitted to progeny. For most genes, many RNA transcripts are synthesized a few defective transcripts are unlikely to be harmful. 

Firstly, electrodeposition makes it possible to fill lithographically defined cavities with nanometer-scale fidelity. This pattern replication capability has been vividly demonstrated in numerous cases [6], even where the cavity depth significantly exceeds its width. Secondly, higher rates of metal deposition can typically be achieved... 

Equation (III.2) may be rewritten to isolate the dependence on the copying fidelity q in order to demonstrate that for a given set of replication parameters there is an error-rate-dependent threshold sequence length for quasi-species instability. To this end the selective advantage or superiority parameter a was introduced ... 

The fidelity of replication is very high with an overall error rate of 10 9 to 10 1°. 

Many DNA polymerases are able to correct mistakes in DNA by removing mismatched nucleotides. These polymerases have a distinct nuclease activity that allows them to excise incorrect bases by a separate reaction. This nuclease activity contributes to the remarkably high fidelity of DNA replication, which has an error rate of less than 10 per base pair. 

RNA viruses like HIV and the influenza virus use a naturally high mutation rate of their RNA polymerases with low fidelity for replication to avoid and escape most treatments and vaccines. A RNA virus tends to mistakenly insert ribavirin into newly synthesized copies of their RNA genome. But ribavirin adds so many extra mutations to the virus during the replication of its genetic materials, it induces a flood of mutations and thus pushes the virus into a kind of genetic meltdown. 

After replication, other mechanisms replace mismatched bases that escaped proofreading so that the fidelity of DNA replication is very high. The two processes of proofreading and postreplication mismatch repair result in an overall error rate of about 10 °, that is, less than one mismatched base pair in 10 billion. 

Role of RNA intermediates (Herbert and Rich, 1999). The mutation rate of a genome is likely to increase when genetic information is passed through RNA whether RNA is a viral genome or a retrotransposon because RNA polymerase reaction is neither edited nor subject to post-replicative repair. In addition, hotspots of a genetic chain in RNA retrotransposons can result from nomandom patterns of a decreased fidelity strand transfer to other templates and untemplated extensions. 

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