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Unspecific binding sites were further blocked in 50% (v/v) FCS, 1% BSA (w/v), and 0.1% (v/v) fish gelatine in PBS (pH 7.4) for 1 h.
In a second experimental step, three putative binding sites were further investigated.
Only pathogen proteins showing at least 80% coverage in their binding sites were further considered (4215).
These binding sites were further compared to the active sites of the template.
When CTCF binding sites were further refined to include only sites coincident with RNA polymerase II binding (CTCF-RNAPII sites), tiRNA enrichments increased considerably, to approximately 45-fold.
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According to the ranking, compound structures and the interactions between compounds and residues in the binding site were further selected for in vivo biological activity assays to assess their inhibitory effect on Dengue virus propagation in cell culture.
Distal p53 binding site was further minimized to 52-mer oligo (probe III) containing consensus p53 binding site and 32-mer (probe IV) deletion mutants, and were used as probe (Figure 4C).
So mut1 binding site was further confirmed by EMSA.
The frog MRP-RNA promoter regions have sequence motifs similar to mammals with a slightly different spacing between the elements within the DSE (the SP1 binding site is further upstream).
The interface of TxIA(A10L) with the principal binding site is further characterized by the formation of four additional hydrogen bonds between TxIA and Pro7-Trp145 (loop B), TxIA and Asn12-Glu191 (loop C), and TxIA Pro7 and Asn11-Tyr193 (loop C).
Then the 19 to 31 bp downstream region of each putative binding site was further scanned for an E. coli -10 σ-70 like box (TAN3T) using a corresponding profile that we have constructed previously from cyanobacterial genomes [ 32], to which a σ-factor of RNA polymerase is likely to bind to transcribe the downstream TU.
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