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. 2020 Jan 16;48(3):1353–1371. doi: 10.1093/nar/gkz1164

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© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — Influence of the ‘−1’ T in the TC target but not the ‘+1’ T in the CT target on APOBEC3 protein activity in an open or stem structure. (A) Oligonucleotide sequence and predicted secondary structure. The ‘half open’ oligonucleotide was designed to contain a T in the TC target site in the ssDNA region and a C in the TC target site of the dsDNA region. The ‘half open’ oligonucleotide contains a C in the CT target site of the ssDNA region and a T in the CT target site of the dsDNA region. (B–E) APOBEC3 protein activity with different oligonucleotide substrates. APOBEC3 activity was analyzed in the presence of half open oligonucleotides with different flanking nucleotides (ATCT VS. ATCG) compared to that of oligonucleotides with an ATCA/ACTA open oligonucleotide or an ATCA/ACTA stem oligonucleotide. Data are shown as the average ± standard deviation from three independent experiments. The asterisks and brackets above any two experiments indicate statistical significance. Significance was analyzed by using a one-way ANOVA with significance defined as P ≤ 0.05. Experiments that were significant or not significant are indicated as follows: ‘ns’ = not significant; ‘****’ = P ≤ 0.0001; ‘***’ = P ≤ 0.001; ‘**’ = P ≤ 0.01; ‘*’ = P ≤ 0.05.

Figure 3. — Influence of the ‘−1’ T in the TC target but not the ‘+1’ T in the CT target on APOBEC3 protein activity in an open or stem structure. (A) Oligonucleotide sequence and predicted secondary structure. The ‘half open’ oligonucleotide was designed to contain a T in the TC target site in the ssDNA region and a C in the TC target site of the dsDNA region. The ‘half open’ oligonucleotide contains a C in the CT target site of the ssDNA region and a T in the CT target site of the dsDNA region. (B–E) APOBEC3 protein activity with different oligonucleotide substrates. APOBEC3 activity was analyzed in the presence of half open oligonucleotides with different flanking nucleotides (ATCT VS. ATCG) compared to that of oligonucleotides with an ATCA/ACTA open oligonucleotide or an ATCA/ACTA stem oligonucleotide. Data are shown as the average ± standard deviation from three independent experiments. The asterisks and brackets above any two experiments indicate statistical significance. Significance was analyzed by using a one-way ANOVA with significance defined as P ≤ 0.05. Experiments that were significant or not significant are indicated as follows: ‘ns’ = not significant; ‘****’ = P ≤ 0.0001; ‘***’ = P ≤ 0.001; ‘**’ = P ≤ 0.01; ‘*’ = P ≤ 0.05.