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HIV-1 has extraordinary potential to generate diversity due to the elevated error incorporation rate of viral reverse transcriptase during the numerous replication events in infected patients.
DNA polymerase V is responsible for error-prone translesion synthesis (e.g., following UV-irradiation), which allows DNA synthesis to proceed despite a high rate of error incorporation [ 32], yet there are organisms, including V. cholerae El Tor, that apparently do not encode these functions [ 33, 34].
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The high rate of nucleotide substitutions detected in Ole e 1 indicates that these substitutions are unlikely to represent in vitro artefacts as the result of error incorporations by the Pfu polymerase used.
The Dpo4 polymerase exhibited primarily an error-free incorporation of dGTP with the 5′-C XG-3′ template.
The sequencing reaction was carried out for each strand of DNA to avoid possible errors of incorporation of nucleotides by Taq polymerase.
Again, the polymerase exhibited low levels of error-prone incorporation of dATP and to a lesser extent, dGTP, opposite to the adduct.
Primarily error-free incorporation of dATP was observed for the 5′-T XG-3′ template (template-primer IV); efficient extension to a full-length 18-mer product was also observed when all dNTPs were included in the reaction.
For a 21-nucleotide-long phosphorothioate-modified oligodeoxynucleotide, we compiled a broad array of error-free incorporations, point mutations, indels, and structural rearrangements from actively dividing HEK293-derived cells.
Of the two, only the polymorphism at position 442 creates a noncanonical pairing, thereby suggesting a possible Taq polymerase incorporation error.
Because the inherited error-prone nature of Tgo DNA polymerase used in preparation of the long PCR templates of HPV58 genome from the clinical samples, the measurable error rate in incorporation of nucleotide into an elongating DNA template was about 0.149% ±0.038% in our studies.
The distribution of sequence variation in the alignment is shown in Table 3, which shows that sequence variation caused by combined PCR nucleotide incorporation error and intra-clonal rDNA polymorphism is low (mean = 0.1%) and that the more rapidly evolving regions of the gene are not more variable in this respect than relatively conserved regions.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com