Interactions of HIV-1 TAR RNA with Tat-derived peptides discriminated by on-line acoustic wave detector

The human immunodeficiency virus type I is strongly regulated at the transcriptional level through the interaction of an 86-amino acid protein (Tat) with a viral messenger RNA transcript. Accordingly, the binding of this protein and other cellular factors to the RNA has constituted a significant target for the development of anti-HIV drugs. In the present work, we describe the detection of the binding of two Tat-derived peptides, of 12 and 40 amino acids in length, with chemically synthesized RNA by an acoustic wave sensor. Immobilization of the nucleic acid to the sensor surface, which was incorporated in an on-line system, was effected using the biotin-neutravidin interaction. As expected, the changes in series resonance frequency and motional resistance for the two peptides indicate reversible interactions in both cases that can be further characterized by the calculation of kinetic off-rates. Of particular interest is the nature of the two frequency-based signals, which are in opposite directions for the two peptides. These results together with those obtained for the surface interactions of neutravidin and biotinylated RNA confirm that the thickness shear mode sensor, mass-response model involving the well-known Sauerbrey expression is invalid when applied to operation in liquids.