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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.
We propose that most reported examples of non-canonical splicing in metazoans arise through template switching by reverse transcriptase during cDNA preparation.
With all RNA samples control reactions without reverse transcriptase during production of the cDNA which was subsequently used in the PCR were performed.
Controls for DNA contamination were performed omitting the reverse transcriptase during reverse transcription.
These biases arise due to the involvement of reverse transcriptase during RTMIL.
Negative control samples (−RT) were prepared by omitting reverse transcriptase during cDNA synthesis.
Similar(44)
Shorter RT-PCR products can also result from intramolecular template switching by reverse transcriptases during cDNA preparation [38], [39].
Because some modified bases are read differently from unmodified bases by reverse transcriptases during cDNA synthesis [ 18], we expect that the modified nucleotides will be read as different nucleotides from genomic ones if the bases of RNAs are modified.
We initially suspected that this resulted from systematic inaccuracy in the refGene 5' annotation due to the reverse transcriptase dissociating during cDNA production.
The differences could be caused either by mismatches introduced by the reverse transcriptase enzyme during library generation, as a result of RNA editing events [ 34, 35] or reflect the natural variation between individual plants and plant parts.
The RNase H activity of reverse transcriptase is required during retroviral replication and represents a potential target in antiviral drug therapies.
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