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This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix.
Our aim was to optimize the assembly efficiency of the AE with a LDP-containing fusion protein and investigate the influence of several factors on the assembly efficacy.
The average assembly efficiency of the unmodified nucleosome reactions from each batch was defined as 1.0 and used as a reference for normalisation.
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As a result, the calculated assembly efficiency (the ratio of the number of supernatant HCV RNA copies to that of intracellular HCV RNA copies) and budding efficiency (the ratio of the HCV titer in the cell supernatant to that in cells) were similar in siRBM24- and siNC-transfected cells (Fig. 1I and 1J).
(I and J) The assembly efficiency (the ratio of the number of supernatant HCV RNA copies to that of intracellular HCV RNA copies) and budding efficiency (the ratio of the HCV titer in the cell supernatant to that in cells) were calculated.
To maximize assembly efficiency, a minimum of 25x and maximum 400x sequence coverage at RAD SE reads were imposed.
While for simulation and assembly efficiency the depths of sequencing we considered are generally lower than for current-generation technologies, we note that our non-normalized 2.2 million simulated read dataset represents over 98% of the D. melanogaster transcript set (see section 'Annotation and rarefaction'), supporting the use of aggressive dataset pruning [ 19].
Using rDNA as integrative locus, this study showed that there was a relation between the assembly efficiency and the length of overlapping region.
The new Figure 6 expands the analysis of the influence of PAL deletion on telomerase activity previously presented in Figure 7D, E. New experiments include side-by-side quantifications of RNP assembly efficiency and specific activity and also the requested time course analysis of repeat addition processivity.
For quantification of programmed assembly efficiency, CellTracker Green CMFDA and CellTrace Far Red DDAO-SE (Invitrogen) stocks were prepared to a concentration of 10 mM in anhydrous DMSO.
This feature allows the use of short (e.g., 16 bp) homologous assembly sequences, and confers high assembly efficiency.
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