Interactions of HIV-1 TAR RNA with Tat-Derived Peptides Discriminated by On-Line Acoustic Wave Detector

Abstract

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.

Influence of viscoelasticity and interfacial slip on acoustic wave sensors

“…However, whether slip occurs when a QCM is operated in a liquid or with a polymer coating is far less certain. Several authors have reported an apparent dependence of the acoustic impedance on the contact angle of the liquid, and hence surface wettability [19][20][21] . Martin et al 22,23 have argued that apparently anomalous results for the acoustic impedance can arise from surface roughness.…”

QCM Technology in Biosensors

“…QCM technology has a huge field of applications in biochemistry and biotechnology. The availability for QCM to operate in liquid has extended the number of applications including the characterization of different type of molecular interactions such as: peptides (Furtado et al, 1999), proteins (BenDov et al, 1997), oligonucleotides (Hook et al, 2001), bacteriophages (Hengerer et al, 1999), viruses (Zhou et al, 2002), bacteria (Fung & Wong, 2001) and cells (Richert et al, 2002); recently it has been applied for detection of DNA strands and genetically modified organisms (GMOs) (Stobiecka et al, 2007). Despite of the extensive use of QCM technology, some challenges such as the improvement of the sensitivity and the limit of detection in high fundamental frequency QCM, remain unsolved; recently, an electrodeless QCM biosensor for 170MHz fundamental frequency, with a sensitivity of 67 Hz cm -2 ng -1 , has been reported (Ogi et al, 2009); this shows that the classical QCM technique still remains as a promising technique.…”

Study on Degradation Characteristics of Chitosan by Pepsin with Piezoelectric Quartz Crystal Impedance Analysis Technique

“…The PQCI analysis technique has been successfully applied to many fields, including the determination of enzyme activity, 16,17 monitoring of the berberine-bovine serum albumin binding process 18 and the interactions between two Tat-derived peptides and HIV-1 TAR RNA. 19 In this work, this technique was successfully used to study the enzymatic degradation characteristics of chitosan under different conditions.…”