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A 105 bp DNA duplex with cohesive ends was generated as described [ 30].
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Carbonyl chloride terminal chain ends were generated using 1% extra sebacoyl chloride that could interact chemically with the organoclay.
In this regard, the observed activation of DNA-PKcs may also reflect that incompatible DNA ends are generated.
The cohesive ends were generated by T4 DNA polymerase (Promega) treatment.
Ligation-proficient SmaI and XhoI restriction ends were generated upon successful annealing of complementary oligonucleotides.
Upon annealing, sticky ends were generated that were suitable for ligation into the pET/T7p/T7 autogene construct cleaved with BglII and XbaI.
Second-strand synthesis was performed using T4 DNA polymerase and E. coli DNA ligase, and then phosphorylated blunt ends were generated using T4 polynucleotide kinase.
Because these sequences occur at what appear to be Piwi-protein-mediated cleavage sites, we speculate that their 3' ends are generated during the same cleavage event that generates the 5' ends of the secondary piRNAs.
The pMCSG plasmids were linearized with the blunt end restriction enzyme SspI, and the sticky ends were generated by T4 DNA Polymerase (NEB, Ipswich, MA, United States) supplemented with 2.5 mM dGTP.
The DNA fragment with the IdU crosslinking reagent at position +2 of the transposon end was generated using the primer pair Tn10Armshort and UCIdUTn10.
It is possible that the hydroxyl end is generated by dephosphorylation.
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