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Since Pfu DNA polymerase generates blunt ends, the PCR product was digested only by SalI and cloned by SalI/Blunt into the pBI Tet vector previously digested by SalI and NaeI (Blunt).
The PvuII endonuclease recognizes a single nucleotide sequence within IS 6110 and generates blunt ends.
Cas9 generates blunt DSBs at sites defined by a 20-nucleotide guide sequence contained within an associated CRISPR RNA (crRNA) transcript (Gasiunas et al., 2012; Jinek et al., 2012).
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Because Phusion DNA polymerase generates blunt-end PCR products, 3' A overhangs must be added to the blunt PCR product before TA cloning.
An RRL was produced from a DNA pool of five boars from a crossbred (Large White vs. Pietrain) commercial boar line (PW), using the restriction enzyme DraI, which recognizes pattern "TTTAAA" and generates blunt-ended fragments starting with AAA.
Positive clones were identified by sequencing; the pshRNA-CX3 or -CX5 vector was digested with XbaI, treated with Klenow polymerase to generate blunt ends, and ligated to a blunt-ended maize ubiquitin promoter fragment to produce pUbi-CX3 or -CX5.
The Δ[−1170 −555] reporter was then treated with Klenow DNA polymerase (Promega) to generate blunt ends and then relegated to generate (fgaB [−555 +1]).
The pET K) was prepared from linearized pET(T), which was prepared by digesting with Tth111I (New England Biolabs), treating with T4 DNA polymerase (Roche) to generate blunt ends and digesting with SapI (Roche).
This method employs SmaI to generate blunt end fragments and to eliminate unmethylated sites (Fig. 3).
Each plasmid was then treated with Klenow polymerase plus dNTPs to generate blunt ends, and subsequently digested with SalI.
To generate the empty control vector pFM18, pSL8 was digested with EcoRI and XbaI, treated with DNA polymerase I (Klenow) to generate blunt ends and then religated.
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