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Hence, the C2576T mutation should occur with a theoretical frequency ranging from 0 85% (average 43%) depending on the template preference for the DNA repair reaction (Figure 1C).
(B ) Template preference of IREF-2-dependent viral RNA synthesis.
DOI: http://dx.doi.org/10.7554/eLife.08939.006 We therefore next examined the template preference of IREF-2.
To adapt this stringent template preference and allow replication of foreign RNAs, pEGX216, a universal mutagenesis vector was constructed based around a small multi-cloning site (MCS) inserted into a modified RQ 135-1 sequence.
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This observation also confirms the template polarity preference of IREF-2.
Furthermore, these bulk PCR assays tend to introduce a number of additional artifacts arising from preferential amplification of small templates (allelic preference), introduction of false deletions through template jumping, and other PCR errors (Kraytsberg & Khrapko, 2005).
This difference could be due to variations in transfection efficiencies compared to the DNA template donor, preferences for longer donor templates for HDR, and/or stability issues.
For BP the caveats include the potential for cross-linking chemistry to be determined by diffusion rather than supramolecular structure, while for PA cross-links can be templated by covalent preference rather than noncovalent structure.
As previously described in several studies including for the E. coli chromosome (Zahra et al. 2007), the orientation with the CAG repeats on the leading-strand template showed a strong preference for large deletions, while the orientation with the CTG repeats on the leading-strand template showed a nearly flat distribution with no strong preference for any particular deletion length.
Partitioning additionally serves to minimize artifacts of template jumping and allelic preference that are common in bulk PCRs (Kraytsberg & Khrapko, 2005).
Some physicians may have a preference for certain templates and select the template based on its content relative to what they already plan to do.
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