Improvement of Electrochemical Response of Cocaine Sensors Based on DNA Aptamer by Heat Treatment

We report on a biosensor for cocaine based on the conformation change of DNA aptamer by capturing the cocaine molecules. The oxidation current of ferrocene conjugated on the terminal end of aptamer immobilized on an Au electrode increased with increasing cocaine concentration. The sensor response has been improved by a simple heat treatment after immobilization, since the aggregates of DNA aptamer generated during the immobilization step could be dissociated and rearranged on the electrode.

RECENT TRENDS IN DNA BIOSENSING TECHNOLOGIES

Recent development and challenges in DNA biosensing technology for the detection of DNA hybridization are reviewed with respect to their abilities to achieve lower detection limit and higher selectivity. Researchers exploit a range of different chemistries for the development of DNA hybridization biosensors, however all the designs take advantage of heterogenous hybridization between the surface-bound DNA (the probe) and the DNA sample (target) in the solution. The detection protocols include using optical, microgravimetry, and electrochemical-based device to transduce DNA hybridization by observing changes in light, mass/frequency, and current/charge, respectively, upon exposure to the sample. The pros and cons of these biosensor designs are discussed with illustrative examples.

Label-free technologies for quantitative multiparameter biological analysis

In the postgenomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We describe the fundamental principles of these different methods and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.

Inhibition of HIV-1 TAR RNA-Tat peptide complexation using poly(acrylic acid)

HIV-1 is regulated at the transcriptional level by the interaction of Tat protein with the transactivation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5'-end of all nascent HIV-1 transcripts. Here, by targeting the Tat peptide, we found that negatively charged poly(acrylic acid) (PAA) had high affinity with Tat peptide and could inhibit the interaction of TAR with Tat. Therefore, PAA could block HIV replication by binding to Tat not to TAR RNA, providing a new thinking for the design of novel anti-HIV drugs.

Quantitative study of HIV-1 Tat peptide and TAR RNA interaction inhibited by poly(allylamine hydrochloride)

The interaction of poly(allylamine hydrochloride) (PAH) with TAR RNA has been studied by quartz crystal microbalance (QCM) cooperating with capillary electrophoresis (CE). Experimental results showed that PAH had high affinity for TAR RNA. In particular, PAH could disrupt the interaction of Tat peptide with TAR RNA, which is critical for HIV-1 virus replication. The approaches described here indicate that they are powerful for studying the binding processes of Tat peptide-TAR RNA and drug-TAR RNA, having great significance for the design of new drug.

Detection of hepatitis B virus by piezoelectric biosensor

A highly sensitive piezoelectric HBV DNA biosensor has been developed based on the sensitive mass-transducing function of the quartz crystal microbalance and the speciality of nucleic acid hybridization reaction. HBV nucleic acid probe was immobilized onto the gold electrodes of a 9 MHz AT-cut piezoelectric quartz crystal with the polyethyleneimine adhesion, glutaraldehyde cross-linking (PEI-Glu) method or the physical adsorption method. The coated crystal with the PEI-Glu method to immobilized HBV nucleic acid probe showed the better results than the physical adsorption method with respect to sensitivity reproducibility and stability. The frequency shifts of hybridization have better linear relationship with the amount of HBV DNA, when the amount was in range 0.02-0.14 microg/ml. The crystal could be regenerated nearly five times without perceptible decrease of sensitivity.

Effect of solvation on induce-fit molecular recognition in supercritical fluid to organic crystals immobilized on a quartz crystal microbalance

The inclusion behavior of guest molecules to a solid apohost of an orthogonal anthracene-bis(resorcinol)tetraol (1) was investigated in supercritical carbon dioxide (scCO(2)) by using a 9 MHz quartz-crystal microbalance (QCM). Compound 1 forms crystals composed of molecular-sheet bound together by an extensive hydrogen-bonded network. The selective binding of gaseous ethyl acetate to the apohost-immobilized QCM in scCO(2) was observed, and the inclusion amount of ethyl acetate showed a drastic increase above a threshold concentration, [Guest](th) = 0.08 M, and the apparent Gibbs' free energy for the binding was DeltaG(app) = -1.3 kcal mol(-1). Similar selective bindings of ethyl acetate or ethanol had been observed in the gas phase and in water: [Guest](th) = 0.002 M with DeltaG(app) = -3.5 kcal mol(-1) and [Guest](th) = 0.5 M with DeltaG(app) = -0.41 kcal mol(-1), respectively. These values obtained in scCO(2) were intermediate between those in the gas and water phases. Since various physical properties (viscosity, density, polarity, diffusion constant, and solvation) of supercritical fluid are known to be intermediate between gas and liquid, these values clearly reflect the solvation behavior of guest molecules. Thus, the lower solvation of guest molecules indicates the lower threshold concentration and the larger binding energy in the following order: in air > in scCO(2) > in water.

Direct monitoring kinetic studies of DNA polymerase reactions on a DNA-immobilized quartz-crystal microbalance

Catalytic reactions of DNA polymerase I from E. coli (Klenow fragment, KF) were monitored directly with a template/primer (40/25- or 75/25-mer)-immobilized 27-MHz quartz-crystal microbalance (QCM). The 27-MHz QCM is a very sensitive mass-measuring device in aqueous solution, as the frequency decreases linearly with increasing mass on the QCM electrode at the nanogram level. Three steps in polymerase reactions which include 1) binding of DNA polymerase to the primer on the QCM (mass increase); 2) elongation of complementary nucleotides along the template (mass increase); and 3) release of the enzyme from the completely polymerized DNA (mass decrease), could be monitored continuously from the time dependencies of QCM frequency changes. The binding constant (Ka) of KF to the template/primer DNA was 10(8)M(-1) (k(on) = 10(5)M(-1)s(-1) and k(off)= 10(-3)s(-1)), and decreased to 10(6)M(-1) (k'on = 10(4)M(-1)s(-1) and k'off = 10(-2)s(-1)) for completely polymerized DNA. This is due to the 10-fold decrease in binding rate constant (k(on)) and 10-fold increase in dissociation rate constant (k(off)) for completed DNA strands. Ka values depended slightly on the template and primer sequences. The kinetic parameters in the elongation process (k(cat) and Km) depended only slightly on the DNA sequences. The repair process during the elongation catalyzed by KF could also be monitored in real time as QCM frequency changes.

Ultrasonic shear wave rheology of weak particle gels

Weak particle gels have attracted increasing attention in the last decade. These gels have a very short region of deformation over which their viscoelastic parameters are constant. They can be broken easily in response to external forces. Therefore the rheological measurements in these systems must be performed at very small deformations, which may frequently be below the accuracy limits of conventional rheological instruments. In the present paper we discuss the application of the thickness shear mode resonator technique for the measurement of viscoelastic parameters of weak particle gels in the MHz frequency range. The technique provides information on the viscoelasticity of weak gels in the time scale 10(-7)-10(-9) s. The length scale of the measurements, determined by the depth of penetration and the wavelength of the shear wave, falls in the submicron and micron range. The displacements in the shear deformations generated in this technique are extremely small, in the order of Angstroms, and the shear strain, approximately 10(-3), corresponds to the low limits in the classical dynamic rheology measurements. Only small volumes, down to 0.1 ml, of sample are required and this is another advantage of this technique. The measurements of the storage, G', and the loss, G'', moduli can be carried out non-invasively and continuously at various frequencies in the same sample during the whole length of the process of gelation. General and specific aspects of the measurements and interpretation of experimental results are discussed in the present paper.

Piezoelectric Mass-Sensing Devices as Biosensors-An Alternative to Optical Biosensors?

In the early days of electronic communication-as a result of the limited number of quartz resonators available-frequency adjustment was accomplished by a pencil mark depositing a foreign mass layer on the crystal. In 1959, Sauerbrey showed that the shift in resonance frequency of thickness-shear-mode resonators is proportional to the deposited mass. This was the starting point for the development of a new generation of piezoelectric mass-sensitive devices. However, it was the development of new powerful oscillator circuits that were capable of operating thickness shear mode resonators in fluids that enabled this technique to be introduced into bioanalytic applications. In the last decade adsorption of biomolecules on functionalized surfaces turned in to one of the paramount applications of piezoelectric transducers. These applications include the study of the interaction of DNA and RNA with complementary strands, specific recognition of protein ligands by immobilized receptors, the detection of virus capsids, bacteria, mammalian cells, and last but not least the development of complete immunosensors. Piezoelectric transducers allow a label-free detection of molecules; they are more than mere mass sensors since the sensor response is also influenced by interfacial phenomena, viscoelastic properties of the adhered biomaterial, surface charges of adsorbed molecules, and surface roughness. These new insights have recently been used to investigate the adhesion of cells, liposomes, and proteins onto surfaces, thus allowing the determination of the morphological changes of cells as a response to pharmacological substances and changes in the water content of biopolymers without employing labor-intense techniques. However, the future will show whether the quartz-crystal microbalance will assert itself against established label-free sensor devices such as surface plasmon resonance spectroscopy and interferometry.

Real-time monitoring of enzymatic cleavage of nucleic acids using a quartz crystal microbalance

The use of quartz crystal microbalance (QCM) for monitoring in situ the enzymatic cleavage of surface-confined nucleic acids by nucleases is described. Such real-time monitoring of mass changes associated with the enzymatic digestion indicates that the activity and specificity of nucleases is preserved at the gold surface, and can be used for manipulating surface-confined DNAs and RNAs. These observations indicate great promise for using QCM for elucidating the interactions of nucleic acids with enzymes, and for enhancing the power of hybridization biosensors.

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.