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Finally, mutant M-1-2 having both polyubiquitin binding sites substituted with alanines was also expressed.
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M-2 has L216ALAL220, a high-affinity polyubiquitin-binding site substituted with alanines.
Therefore, we created the following mutants of angiocidin based on the polyubiquitin binding structure of S5a: M-1 has I290AYAM294, a low-affinity polyubiquitin-binding site substituted with alanines.
M-1-2 has both sites substituted with alanines.
Using the mutagenic PCR method, random nucleotides in the binding site were substituted with different nucleotides to impair HOXD10 binding.
Ala290 at the interface of ThMA dimer in the vicinity of the substrate-binding site was substituted with isoleucine, which may cause a structural change due to its bulky side chain.
Two RAP1 binding sites can substitute for the wild-type initiation site.
In particular we asked whether the ultra-conserved Rap1 binding site in silencers, if substituted with the genome-wide consensus binding site of Rap1, could maintain its native level of performance in silencing.
Mutagenesis was performed using a QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla, CA, USA), and all the adenines of miRNA-binding sequences were substituted with thymines.
For RNA-binding experiments, Cy5-dT15 wasubstituteded with 5′-Cy5-rUrUrUrUrUrUrUrUrUrUrUrUrUrUrU-3′ (Cy5-rU15).
The R5 site was mainly substituted with hydrogen atoms or oxymethyl (-OCH3) groups.
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