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No binding was obtained using pre-immune serum or Protein G-Sepharose beads only as negative controls.
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In particular, significant relationships between experimental and computed free energies of binding were obtained using Amber PBSA and structures minimized with a distance-dependent dielectric function.
A similar allele-specific binding pattern was obtained using nuclear extract derived from human THP-1 cells (data not shown).
The mutated MAFB 3'UTR containing mutations of the miR-223 binding sit was obtained using GeneTailor Site-Directed Mutagenesis System (Invitrogen), namely mutated 3'UTR (mt-UTR).
A deletion for the let-7e predicted binding site was obtained using the QuickChange II XL site-directed mutagenesis kit (Stratagene, Santa Clara, CA, USA).
A binding site residue selection was obtained using the program JOY [47].
The apparent binding constant of each variant was obtained using six analyte concentrations (2 – 20 nM).
The KD value for binding to the CRISPR4 target was obtained using the Densitometric Image Analysis Software, available at http://micr.vub.ac.be.
A possible binding mode for the compound was obtained using the program GOLD version 2.1 and the structure of Akt PH domain (PDB code: 1H10) 36.
Further evidence of the binding of HAMLET to proteasome subunits was obtained using a protein array.
Mutant ΔNp63 3'-UTR, which carried a substitution of four nucleotides (CTTT to GAAA) within the core binding sites of ΔNp63 3'-UTR (14), was obtained using overlapping extension PCR.
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