Figure 1.
Schematic representation of the model system.
The library preparation consists of six steps, beginning by extending randomized synthesized oligonucleotides (1), digesting the extended constructs (2), enriching the constructs and removing cleaved products (3), ligating sequencing adapters to the cleaved fragments (4), denaturing single stranded DNA from beads (5), and amplifying with PCR for sequencing (6).
Table 1.
Reaction conditions for each enzyme used in the study.
Figure 2.
Slippage distributions for the Type IIS enzymes tested.
Bar plots showing the percentage of reads obtained at the expected distance (0) and +/− 2 bp away for different Type IIS enzymes. The enzymes display a wide range of length specificity but usually not more than 1 bp away from the preferred distance.
Table 2.
Distribution of total slippage detected of the restriction enzymes.
Figure 3.
Slippage and sequence dependence of isoschizomers FauI and SmuI.
Sequence logos were generated showing the most frequent base per position (in bits) in the region between recognition and cleavage. The detected slippage from −2 to 2 bp are shown independently (row 1 through 5). Recognition site is not included in the plot but was identified immediately left to the plots shown. In the corner the number of sequences identified (and used for the plot) and the relative frequency for that enzyme are shown.