RNA-peptide binding and the effect of inhibitor and RNA mutation studied by on-line acoustic wave sensor

Acoustic wave devices of the transverse shear-wave type are becoming increasingly important in the study of biochemical binding events at the solid-liquid interface in real time. The operation of the sensor is based on the principle that perturbations occurring at the solid-liquid interface result in changes in the propagating characteristics of the acoustic wave. The binding of the human immunodeficiency virus-type 1 Tat protein to the transactivation-responsive RNA element has been studied using this sensor. Variable acoustic signals in terms of frequency and motional resistance changes are obtained when surface-immobilized RNA is challenged by different peptide fragments derived from Tat protein. The effect of peptide concentration and mutation in addition to the inhibition of RNA-peptide binding by neomycin has been investigated. The results of this study suggest that acoustic physics offers considerable potential for the screening of small-molecule interactions with nucleic acids.