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Previous studies demonstrated that such recombination in vivo requires the bottom strand of the attC [10].
Our results indicate that in vitro attC recombination requires the bottom strand of the site in contrast to attI recombination.
In most reactions, the 5'-OH on the bottom strand of the half-site was blocked by phosphorylation (Figure 2B) to prevent the strand joining reaction.
Recent data have shown that its recombination specifically involves the bottom strand of the attC site, but the exact mechanism of the reaction is still unclear.
Structural studies and in vivo recombination models demonstrated that IntI1 recombines the single bottom strand of the attC sites (bsattC), folded in an imperfect hairpin structure with extrahelical bases, and the double strand (ds) attI1 substrate [9], [10].
According to the Target primed Reverse Transcription model, retrotransposition is initiated by the LINE-encoded Endonuclease (EN) nicking the bottom strand of the target site [ 15].
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We assessed the symmetry of specific cleavage by investigating IN activity on the other (bottom) strand of this palindrome (PalA; Fig. 2A, lanes 8 10).
Consistent with this hypothesis, a study by Vu et al.[ 31] examined DNA methylation on the top and bottom strands of the human Igf2/H19 imprinted region.
For the predicted let-7 and miR-72 Ciona miRNA homologs, oligonucleotides were designed as probes for both the top and bottom strands of the hairpin structure.
To validate the strand polarity of the predicted mature miRNAs, we performed the Northern blot analysis with sense and anti-sense probes for the top and bottom strands of the let-7 and miR-72 C. intestinalis homolog predictions.
The 3'OH ends join to staggered positions on the top and bottom strands of the target DNA, followed by repair of the resulting gaps (Craigie and Mizuuchi 1985; Craig et al. 2002).
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