SELEX-seq (Systematic Evolution of Ligands by EXponential enrichment) assay starts from a semi-random DNA library of p53 response elements (R0). The DNA library is incubated with p53 and loaded on EMSA gel for selection of bound DNA-p53 complexes. Bound complexes are eluted and PCR-amplified for subsequent rounds of selection (R1…Rn). Initial DNA pool (R0) and selected DNA pools (R1…Rn) are sequenced separately using next generation high-throughput sequencing after incorporating a unique adapter and barcodes to each DNA fragment using limited-cycle PCR.
The following step is data analysis, calculating the relative affinity for any DNA variant and characterizing p53 binding site preferences.
