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BisQ is marked in blue B; the mismatch is marked in red. The unstacked base pair steps (BPSs) due to the mismatch are boxed. The DNA base triads opposite to BisQ are underlined. When the mismatch is situated 5′ to BisQ (R), the resulting unstacking occurs within the BisQ opposite to the DNA triad. In contrast, in the L case, the unstacked BPS is outside of the BisQ opposite to the DNA triad.
