Fragment FP1 and its derivatives FP1-1 and FP1-2 (Fig. 2a) containing either the distal or the proximal half of the palindrome were used for EMSA. Fragment FP1-3, which contains 2 U of the distal half,

and fragment FP1-4, which contains 2 U of the proximal half of the palindrome in direct repeats separated by GGC, were also used (Fig. 2a). Results indicated that DNA fragments containing only the distal or the proximal half as well as those containing two copies of distal or proximal half of the sequence were not bound by the PhaR protein (Fig. 2b). The PhaR protein bound only to the DNA fragment containing the sequence in its native configuration. Thus, both halves of the palindrome are required for Palbociclib cell line formation of a stable PhaR–DNA complex, and the orientation of the motif is critical for efficient binding of the PhaR protein. To determine the nucleotides within the sequence −71TTCTGCGGCGCAGCA−57 that are required for PhaR binding, various deletions including the T residue at position −71 and A at position −57 (Fig. 2a, FP1-5), both Ts at positions −70 and −71, and both the C residue at position −58 and the A residue at positions −57 (Fig. 2a, FP1-6), were performed. None of these deletions were found to have any effect on PhaR

binding (Fig. 2b). However, deletion of the first GSK2118436 nmr three nucleotides from both ends (Fig. 2a, FP1-7) abolished PhaR binding. Therefore, the PhaR-binding sequence was narrowed down to the 11-bp CTGCGGCGCAG symmetrical palindrome. Because the PhaR-binding sequence identified in this study is novel, careful analyses were performed to determine the importance of each nucleotide in the sequence for PhaR binding. A series of base substitutions were generated in either half of the CTGCGGCGCAG motif, including changing the first four bases from CTGC to ATGC, CAGC, CTAC, or CTGA and the last four bases from GCAG to GCAT, GCTG, GTAG, or TCAG (Fig. 2a, FP1-8, FP1-9, FP1-10, and FP1-11). All of these mutations were found to abolish PhaR binding (Fig.

2b). To investigate the importance of the three spacer nucleotides GGC in PhaR binding, the first G (Fig. 2a, FP1-18), both Gs (Fig. 2a, FP1-19), or the entire GGC (Fig. 2a, FP1-20) were deleted. Calpain All of these deletions abolished PhaR binding. Thus, the 3-bp spacing between the two halves of the palindrome is important for PhaR binding. To determine whether the spacer region must be GGC, it was replaced by GGT (Fig. 2a, FP1-12), GGA (Fig. 2a, FP1-13), GGG (Fig. 2a, FP1-14), CAT (Fig. 2a, FP1-15), ATG (Fig. 2a, FP1-16), or AGCC (Fig. 2a, LM17), and all of these mutations were found to have no effect on PhaR binding (Fig. 2b). These results indicated that PhaR recognizes a specific sequence, but the spacer region can be any three or four nucleotides.