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The TAP-tagged versions of the Importin proteins and nucleoporins were generated as follows: the TAP-tag sequence (streptavidin-binding and calmodulin binding peptides) were amplified by PCR from the InterPlay™ vector pCTAP-A (Stratagene) and cloned downstream of the recombination site of the pDEST14 Gateway™ vector (Invitrogen).
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After ChIP assays the immediate 5′ upstream sequences containing putative NF-κB-binding elements were amplified from human genomic DNA.
Sequences corresponding to the antigen-binding domain were amplified and cloned in a phage display vector.
NprB signal peptide fragments were amplified from the genome of Clostridium thermocellum DSM 1237.
The 1183 predicted HLA-binding peptides were synthesized and used to generate individual pMHC monomers using UV-mediated peptide exchange32.
After 4 5 rounds of biopanning against the surface-immobilized target proteins, phages binding to KDM1 and -4 proteins were amplified in E. coli, and phage-ELISA revealed a number of potential KDM1 and -4 interacting peptides (PP1 6, Table 1).
The DNA fragment encoding Ydj1 peptide binding domain (102-384) wamplifiedied from Ydj1 cDNA by PCR.
A 3HA peptide coding sequence and URA3 selection marker were amplified from a pRS416-based plasmid (kind gift from Dr. Xuetong Shen).
Positives clones were amplified and sequenced to deduce their peptide insert.
The 3' UTR of MYH9 containing let-7f binding site was amplified by PCR.
In contrast, MHC-binding peptides are highly stable.
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