Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

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

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 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

PMC Copyright notice

Figure 4. — APOBEC3 proteins prefer a TC target site in ssDNA rather than in the context of a loop or a bulge. (A) Oligonucleotide sequence and predicted secondary structure. The ‘10-loop’ oligonucleotide contains the TC target site in a 10nt ssDNA loop. The ‘3-loop’ oligonucleotide contains the TC target site in a 3nt ssDNA loop. The ‘Bulge’ oligonucleotide contains TC target site in a ssDNA region with flanking bases in a dsDNA region. The ‘X’ represents the flanking bases (‘A’ or ‘G’). (B–G) APOBEC3 protein activity with different oligonucleotide substrates. APOBEC3 activity with oligonucleotides containing the target site either within a large region of ssDNA (10-loop), within a small region of ssDNA (3-loop) or a bulge was compared to that of the target site in an open TC. Data is shown as the average ± standard deviation of three independent experiments. Significance was analyzed by using a two-way ANOVA with significance defined as P ≤0.05. Significant differences between experiments of an open structure compared to another secondary structure is indicated by a ‘*’ above relative histogram bar. The ‘+’ symbol and brackets above any two bars indicates the significant difference between analyses. Experiments that were significantly different are indicated as follows: ‘****’/ ‘^{+ + + +}’ = P ≤ 0.0001; ‘***’/ ‘^{+ + +}’ = P ≤ 0.001; ‘**’/ ‘^{+ +}’ = P ≤ 0.01; ‘*’/ ‘⁺’ = P ≤ 0.05.

Figure 4. — APOBEC3 proteins prefer a TC target site in ssDNA rather than in the context of a loop or a bulge. (A) Oligonucleotide sequence and predicted secondary structure. The ‘10-loop’ oligonucleotide contains the TC target site in a 10nt ssDNA loop. The ‘3-loop’ oligonucleotide contains the TC target site in a 3nt ssDNA loop. The ‘Bulge’ oligonucleotide contains TC target site in a ssDNA region with flanking bases in a dsDNA region. The ‘X’ represents the flanking bases (‘A’ or ‘G’). (B–G) APOBEC3 protein activity with different oligonucleotide substrates. APOBEC3 activity with oligonucleotides containing the target site either within a large region of ssDNA (10-loop), within a small region of ssDNA (3-loop) or a bulge was compared to that of the target site in an open TC. Data is shown as the average ± standard deviation of three independent experiments. Significance was analyzed by using a two-way ANOVA with significance defined as P ≤0.05. Significant differences between experiments of an open structure compared to another secondary structure is indicated by a ‘*’ above relative histogram bar. The ‘+’ symbol and brackets above any two bars indicates the significant difference between analyses. Experiments that were significantly different are indicated as follows: ‘****’/ ‘^{+ + + +}’ = P ≤ 0.0001; ‘***’/ ‘^{+ + +}’ = P ≤ 0.001; ‘**’/ ‘^{+ +}’ = P ≤ 0.01; ‘*’/ ‘⁺’ = P ≤ 0.05.