Ideally yes. If your protein binds your 12 bp sequences, chances are it will bind 50bp or 100bp or more if it contains the same binding sequence.

You can also play with the percentage of your gel to better resolve small differences (I use 15% Tris-Glycine gel for 25 bp probes), or use longer gels to let it migrate more. Some buffers also allow better resolution in the low-weight range.

Martin Chenal Thank you.

For most transcription factors 12 bp is not enough even if this sequence covers all specific base contacts. Additional ionic interactions with the phosphate backbone stabilize the interaction. I agree with Martin Chendal and would go for a 25 bp probe. This is a typical size protected in a DNAseI Footprint.

Uwe Borgmeyer Thank you for your answer.