Immobilize the protein on a solid support. This is easiest if the protein has an affinity tag and you use the corresponding affinity resin. Mix the protein resin with the mixture of oligonucleotides. Wash the resin to remove unbound nucleotides. Elute the bound nucleotides from the resin, probably by using high salt or low pH, or even boiling to denature the protein. Pellet the resin and collect the supernatant. Analyze the supernatant (by sequencing, probably) to determine which oligos are present.

Adam B Shapiro Thank You

To add to Adam's answer, you could also use protein A/G Magnetic beads pre-bound to an antibody targeting your transcription factor.

Yahong Wen Thank You for your input