Journal: Microbial Cell Factories

Article Title: A high-throughput, restriction-free cloning and screening strategy based on ccd B-gene replacement

doi: 10.1186/1475-2859-13-38

Figure Lengend Snippet: Numbers for ccd B counterselection with or without Dpn I for the targets and cloning protocols used

Article Snippet: For Dpn I treatment, 20U enzyme (NEB) was added directly to half of the PCR product and incubated at 37°C for 30 minutes.

Techniques: Clone Assay

Journal: BMC Genomics

Article Title: Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans

doi: 10.1186/1471-2164-11-465

Figure Lengend Snippet: Copy number determination for lines PD3994 and PD5122 . Panels a, c, e, g, and i are agarose gel images of Dpn I , Mbo I , and Sau3A I digested DNA from PD3994, PD5122, and N2 (control) animals. Below each agarose gel is the corresponding Southern blot (b, d, f, h, j). pPD98.38 is a plasmid from which the probe (808 bp of the C. elegans 5S rDNA/SL1) was synthesized. The slight smearing seen in ethidium bromide stained gels for N2 (a and e) likely resulted from non specific activity of Dpn I . Compared to fully methylated GATC, Dpn I can cut non-methylated GATC 1,000 fold slower and hemimethylated GATC 60 fold slower (Derek Robinson, New England Biolabs, personal communication).

Article Snippet: Ligation to Linker A was carried out in a 50 μl reaction using the following mix: 10 μl Dpn I product, 1.5 μl of 0.05 mM Linker A, 11.0 μl dH 2 O, 25.0 μl 2× Quick Ligase Buffer, 2.5 μl Quick Ligase (NEB #M2200).

Techniques: Agarose Gel Electrophoresis, Southern Blot, Plasmid Preparation, Synthesized, Staining, Activity Assay, Methylation