Once the consensus nucleotide sequence was obtained and the primer binding sites excluded, the Clustal W option in MEGA 4.0 was used to deduce the corresponding amino acid sequence and to construct an unrooted neighbor-joining tree.
The majority of binding sites (excluding DnaA_2 and CtrA_2) occur within a region that experienced a similar low number of recombination events, suggesting that usually these sites, when recombining, are exchanged as a unique sequence tract.
The side chains of Pro(Ser)92, Leu52, and Val81* enclose the binding site, excluding solvent.
Measurement of Mre11 binding adjacent to TG tracts of varying length suggests that long arrays of Rap1-binding sites exclude Mre11 through a Rif-independent mechanism either intrinsic to Rap1, or operating through an unidentified interacting partner (Negrini et al, 2007).
This revealed no cell line-derived sequence variability within the identified binding sites, thus excluding sequence variation as explaining the observed deviation in mtDNA binding among the tested cell lines.
However, structural information for CMPKother, E2 31other and Survivinother sites are not publicly available, and the crystal structure of MurA is fosfomycin-covalent modified, so these 4 binding sites were excluded in our study.
To confirm this, rate limiting qPCR was performed using DNA immunoprecipitated from nitrogen limiting and excess conditions, and no enrichment was observed (data not shown), therefore this binding site was excluded from the GlnR regulon.
For example, I excluded the Bcd binding sites in the eve stripe 2 enhancer and reconstructed the Bcd matrix for analysis of that regulatory region.
The possibility that Wg-stabilized Mad may bind to Armadillo/β-catenin, Pangolin/lef1, Legless/bcl9 and Pygopus independently of nearby Mad binding sites cannot be excluded at present.
Two of the Kr and Bcd binding sites the eve stripe 2 enhancer overlap, and I excluded two substitutions that affect the strength of more than one binding site (Table 3).
