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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.
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.
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.
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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).
Following overnight digestion, reactions were digested further with 5 uL (50U) of TspRI (NEB) at 65°C for three hours.
Splitting samples into three reactions and digesting each reaction with one of three 4-base recognition sequence restriction enzymes allowed fragmentation of DNA while maintaining high representation of genome sequences in fragments > 100 bp.
For total genomic methylation studies, digested gDNA reactions were first diluted tenfold in water.
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