Detection of oligonucleotide systematic mismatches with a surface plasmon resonance sensor

The detection and parallel characterization of the hybridization event of 21-base, unlabeled DNA oligonucleotides with a monolayer of complementary DNA immobilized on a gold surface by surface plasmon resonance (SPR) is presented. A thiol modification on the probe DNA strand allowed for its attachment to the surface via self-assembly. For the hybridization of full match DNA a detection limit of 20 pM was determined. The change in SPR signal was always larger for the full match compared to the one-mismatch target DNA oligonucleotides when the mismatch was in the middle or at the proximal end of the target DNA. Hybridization conditions (buffer concentration, flow rate, and temperature) did not affect the ability of the sensor to discriminate for single nucleotide mismatches. To our knowledge this is the only work where a comparison on the surface hybridization efficiency is performed between proximal, distal, and middle mismatches and the effect of three hybridization parameters is studied with regard to the detection of single nucleotide mismatches using SPR.