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The restriction enzyme was heat inactivated and a 16SPLSUFwd/16SPLSURv PCR performed with 2.5 µl of template DNA taken directly from the restriction digest reaction (see below).
After restriction digestion (100 ng of plasmid DNA and 0.5 U of Asc I or Srf I in 10 μL total volume), 1 μL of the digest reaction (~20 ng DNA) was re-ligated with Fast-Link™ ligase (Epicentre Technologies) for 15 min at room temperature (0.5 mM ATP, 1X Fast-Link™ buffer, 1 U ligase, 7.5 μL total volume).
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In order to confirm recombination of the ccdB gene with the gene of interest, plasmids were digested with BsrGI (NEB, UK), and digest reactions analyzed by gel electrophoresis.
In general, restriction digest reactions to screen for mutations, were incubated for 1 3 hr at 37° and heat-inactivated if necessary according to the manufacturer's instructions.
Digest reactions included the use of trypsin digestion alone; trypsin digestion followed by Glu-C digestion; Asp-N digestion followed by Arg-C digestion; or Asp-N/Arg-C digestion followed by Glu-C digestion.
RADseq libraries were prepared by single digest reactions using PstI, combinatorial inline barcoding, and size selection with magnetic beads.
The digest reactions were analyzed in an 8 16% polyacrylamide gradient gel.
The irradiated splenocytes from B10.PL mice (1×106) were co-incubated for 1 h with the digest reactions.
There were no cleavage sites in the biosensor additional to the linker and, as a result, only the cleavage products that corresponded to the ECFP and YPet moieties were observed in the digest reactions.
The digest reactions were phenol : chloroform extracted and ethanol precipitated.
The restriction enzymes and expected digest band sizes for each PCR-RFA are listed in Table 2. Amplified products from M. tuberculosis H37Rv and a second appropriate MTC species (see above) were included in all digest reactions as controls.
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