Influence of dsDNA fragment length on particle binding in an evanescent field biosensing system

Particle labels are widely used in affinity-based biosensing due to the high detection signal per label, the high stability, and the convenient biofunctionalization of particles. In this paper we address the question how the time-course of particle binding and the resulting signals depend on the length of captured target molecules. As a model system we used fragments of dsDNA with lengths of 105 bp (36 nm), 290 bp (99 nm) and 590 bp (201 nm), detected in an evanescent-field optomagnetic biosensing system. On both ends the fragments were provided with small-molecule tags to allow binding of the fragments to protein-coated particles and to the capture molecules at the sensor surface. For isolated single particles bound to the surface, we observe that the optical scattering signal per particle depends only weakly on the fragment length, which we attribute to the pivoting motion that allows the particles to get closer to the surface. Our data show a strong influence of the fragment length on the particle binding: the binding rate of particles to the sensor surface is an order of magnitude higher for the longest dsDNA fragments compared to the smallest fragment studied in this paper. We attribute the enhanced binding rate to the length and motional freedom of the fragments. These results generate a new dimension for the design of assays and systems in particle-based biosensing.