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Under the ESDSA, DSB fragments formed in irradiated D. radiodurans are first subject to a 5'→3' exonuclease resection mechanism that generates overhanging 3' tails.
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Spe I generates identical overhanging ends as Nhe I and facilitates ligation of the Nhe I/Asc I fragment containing GPT into the vector with destruction of both Spe I and Xba I restriction enzyme sites.
Although this method demonstrated high efficiency for complete multiple mutagenesis, synthesis of phosphorothioate nucleotides is necessary to generate 3′-overhanging DNA fragments.
In this technique, genomic DNA is digested to yield overhanging sticky ends (Figure 1B).
For each of these, we randomly generated sequences with mismatches and overhanging ends, so that the number of center sequences was the number of true clusters.
The PCR products were digested with NotI and XbaI restriction enzymes to generate the appropriate overhanging sequences.
The acceptor DNA was amplified with a 5′-biotinylated oligonucleotide and unlabelled primers, was cleaved with a non-palindromic restriction enzyme to generate a 3′-overhanging sequence that was complementary to the overhanging sequence on the first donor DNA molecules, and was then attached to the streptavidin beads.
FEN1 is an endonuclease that cleaves the 5′ end overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5′ end of a downstream Okazaki fragment.
The spPCR method requires a sticky end generated by a Class II restriction endonuclease with 5' overhanging nucleotides [9].
Cleavage at such sites can generate any desire 3′-overhanging single-stranded sequences; these overhangs are derived from the bp in the middle of the recognition site.
Enzyme Avr II contains overhanging ends that are compatible with Spe I which facilitated the ligation of the SE/L-luciferase fragment into the pGPT/PCSII plasmid to generate pGPT/luc/PCSII construct.
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