Figure 1.
Detection of the DNA-binding affinities of the NF-κB p50 homodimer to a wild-type binding site (GGGACTTTCC) and its all single-nucleotide mutants with the bimolecular dsDNA microarray.
The florescence image is a representative result of the dsDNA microarray detections. Each feature is composed of a bimolecular dsDNA probe. The sequences of the sense strands of each dsDNA probes are displayed under the image. All probes were arrayed in triplicate (each column) and the wild-type probe was arrayed in triplicate before the three mutants of each position. The positions of NF-κB binding sites were labeled as numbers of 1 to 10 after the bases.
Table 1.
The single-nucleotide mutant matrix (SNMM).
Figure 2.
A, Correlations between the EMSA values and the scores of the PC, SNMM, PWMSA, and Match models, respectively. B, Correlations between the PBM z scores and the scores of the PC, SNMM, PWMSA, and Match models, respectively. C, Correlations between the SELEX-Seq values and the scores of the SNMM, PWMSA, Match, and PC models, respectively. Correlation between the SELEX-Seq values and the EMSA values. **, p<0.01. P value refers to the confidence interval of Pearson's r. The number under the abscissa refers to the number of values or sequences used in the corresponding correlation analysis.
Table 2.
The EMSA values and model scores of NF-κB to 52 sequences.
Figure 3.
Detection of the DNA-binding affinities of the NF-κB p50 homodimer to four sequences with NIRF-EMSA.
A, A representative image of the NIRF-EMSA detections. B, The quantified signal intensities of the shifted bands (labeled as DNA/p50 complex in Image A). a, GGGGATTCCC; b, GGGATCTCCC; c, GGGATACCCC; d, GGGAGGCCCC.
Figure 4.
The relative binding affinities of the NF-κB p50 homodimer to four variant sequences.
A, The binding affinities of the NF-κB p50 homodimer to four sequences detected with the radioactive EMSA (R-EMSA), NIRF-EMSA (N-EMSA) and SELEX-Seq (SELEX), respectively, and scored with the SNMM, PWMSA, Match and PC models, respectively. B, The correlation between the EMSA-detected values and the model scores. *, p<0.05; no *, p>0.05. P value refers to the confidence interval of Pearson's r.