A modified sensor chip for surface plasmon resonance enables a rapid determination of sequence specificity of DNA-binding proteins

Abstract

A novel method is described which rapidly determines specificity of DNA-binding proteins using a surface plasmon resonance (SPR) sensor chip. An oligohistidine-tagged DNA-binding domain of a transcription factor, NtERF2, was immobilised via nitrilotriacetic acid ligands to a sensor chip with an attenuated degree of carboxymethylation. DNA molecules were selected from a pool of randomised oligomers through binding to the immobilised protein and amplified by PCR. After several cycles of selection, during which binding was monitored by SPR, DNA sequences containing a consensus sequence were determined. The time necessary for one cycle is approximately 50 min, which is shorter than existing methods.