  Surface plasmon resonance (SPR)-based biosensors are widely used instruments
for characterizing molecular interactions. In theory the SPR signal depends
only on mass changes for interacting molecules of same chemical nature. Whether
conformational changes of interacting molecules also contribute to the SPR
signal is still a subject of lively debates. Works have been published claiming
that conformational changes were detected but all factors contributing to the
SPR signal were not carefully considered, in addition to often using no or
improper controls. In the present work we used a very well-characterized
oligonucleotide, the thrombin-binding DNA aptamer (TBA), which upon binding of
potassium ions folds into a two G-tetrad antiparallel G-quadruplex structure.
All terms contributing to the maximal expected SPR response, Rmax, in
particular the refractive index increment, RII, of both partners and the
fraction of immobilized TBA target available, ca, were experimentally assessed.
The resulting Rmax was then compared to the maximal experimental SPR response
for potassium ions binding to TBA using appropriate controls. Regardless how
the RIIs were measured, by SPR or refractometry, and how much TBA available for
interacting with potassium ions was considered, the theoretical and the
experimental SPR responses never matched, the former being always lower than
the latter. Using a straightforward experimental model system and by thoroughly
taking into account all contributing factors we therefore conclude that
conformational changes can indeed contribute to the measured SPR signal.
