These HSEs have binding affinity comparable to the minimal functional binding sequence as long as they exceed 4 subunits [20].
To assess the effect of USP7 on p53 DNA binding, we conducted electrophoretic mobility shift assays (EMSAs) using a Cy-5 labeled consensus p53 binding sequence as a probe and a version of p53 spanning the core DNA binding and the C-terminal regulatory regions (p5382 393) but lacking the transactivation domain, (Figure 1A).
We treated the mapping between transcription factors and binding sequences as a coding problem, where the code-words are short DNA sequences of a given length and the messages are TFs.
As one possible explanation, we consider the mapping of transcription factors to binding sequences as a coding problem, analogous to the assignment of amino acids to codons in the genetic code.
Then, we used a surface plasmon resonance (SPR) biosensor to test 3 mutant sequences of high ZRANK scores along with a high and a low affinity binding sequence as reported in the literature.
When determining the overlap between genes annotated with a select IPA term and genes containing a selecting binding sequence (as determined by GATHER), the gene symbols were first converted into unique gene identifiers using the DAVID gene ID converter.
Nucleotide sequences of the oligonucleotides containing an Egr-1 consensus binding sequence as reported by Santa Cruz Biotechnology SC-25299) are 5′-GGATCCA GCGGGGGCGA GCGGGGGCGA-3′ and 3′-CCTAGGT CGCCCCCGCT CGCCCCCGCT-5′.
The effects of the substances on the basal transcriptional activities of AP-1, NF- κB, or p53 nuclear factor were evaluated using JB6 cell celinesnestablyly expressing a luciferase reporter gene controlled by an AP-1-, NF- κB-, or p53-DNA binding sequence, as described previously [ 14].
We used the E2F4 binding sequence as derived by [41], based on the positional weight matrix model [44] of binding specificity.
II) It contains a recognition sequence for the Mly I restriction enzyme (Mly I is, to our knowledge, the only commercially available enzyme which cleaves blunt end outside its binding sequence, as required here).
