Acoustic wave biosensor for detecting DNA conformation; A study with QCM-D

Abstract

This work describes the development of a real-time rapid technique for the quantitative characterization of DNA intrinsic curvature and conformational changes. We present a new approach where a label-free acoustic biosensor (QCM-D) is used for the detection of DNA conformation independently of bound DNA mass. DNA molecules bind to a neutravidin modified device surface by use of a biotin linker. Acoustic results, expressed as the ratio of dissipation over frequency change, DeltaD/Deltaf, provide insight on (intrinsic) viscosity changes [eta] occurring at the sensor/liquid interface as a result of DNA binding. Quantitative results regarding both the size and shape of DNAs were obtained, for the first time, by combining acoustic measurements with a mathematical treatment of solution viscosity theory. More specifically, we show that: DeltaD/Deltaf ~ [eta]. Acoustic measurements can clearly distinguish between ds-DNAs of same shape (rod) but various sizes (lengths of 20 up to 198 bp) and, of same mass and size (90 bp) but in various shapes (ldquostraightrdquo, ldquobentrdquo, ldquotrianglerdquo). Our results agree well with published qualitative observations and suggest that acoustic biosensors can be developed into a powerful tool for studying DNA conformational changes.