Genomic DNA hybridizes with the same rate constant on the QCM biosensor as in homogeneous solution.

Hybridization rates of sheared, genomic E. coli DNA in 0.14 M, pH 6.7 phosphate buffer at 65 degrees C were determined by: (1) observing the rate of absorbance decrease at 260 nm due to self-hybridization in solution; and (2) measurement of the rate of mass increase caused by hybridization between DNA in solution and DNA photografted to polystyrene. The latter measurement was done using a quartz crystal microbalance (QCM). In both the spectrophotometric and QCM experiments the probe was identical to the target, as both were taken from the same sample of sheared E. coli DNA. In the QCM measurements, viscoelastic effects were made negligible by drying the biopolymer layer on the QCM's surface before taking the frequency readings. Our purpose was to explore the effect of immobilizing DNA on its hybridization rate constant. A second-order constant of 2.32 +/- 0.09 x 10(-6) ml microg(-1) s(-1), n = 14, for hybridization in solution was obtained spectrophotometrically, while the QCM experiment gave a constant of 2.2 +/- 0.3 x 10(-6) ml microg(-1) s(-1), n = 6. These values are not statistically different. The reaction half-lives for the spectrophotometric and QCM experiments were 6.5 h and 13 min, respectively. The shorter half-life on the QCM can be explained solely by the much greater reactant concentration in the QCM experiment. About 25% of the DNA was inactivated by the attachment reaction. After correcting for this, the surface-attached DNA hybridized with the same rate constant as DNA free in solution. Therefore, it is concluded that, in these specific experiments with genomic DNA, the immobilized regions must have been short compared to the length of the molecules. The data demonstrate the high hybridization rate obtainable when nucleic acids are hybridized in a thin-film, micro-volume reaction on a non-porous surface.

Rapid SLT gene detection on polyethylene-coacrylic acid film without molecular labels or surface-fouling agents.

The commercially available copolymer of 10 mol% acrylic acid and polyethylene is easily formed into a nonfluorescing, non-polynucleotide-adsorbing film. The film has surface carboxylate functions whose concentration can be increased by heating to 80 degrees C in 30% NaOH. The carboxylate groups will react at pH approximately 7 with commercially available, oligo-DNA, 2-8 ng/microl, that has been synthesized with a C(12)-alkylamino tail on the 5'-end. The reaction is mediated with water-soluble carbodiimide reagent and is assumed to result in a primary amide bond between the polymer film and the modified oligo-DNA. The tethered oligo-DNA retains its hybridization activity, and its surface concentration is sufficient to permit qualitative, labelless detection of hybridized target by fluorescence after brief staining with ethidium bromide. The film is used to detect Shiga-like toxin gene II (SLT-II) from Escherichia coli O157:H7 after asymmetric, capillary, PCR amplification, and a 4-h hybridization. Captured target may be removed from the film using distilled water, after which the film can be used again without noticeable loss of activity. The method provides relatively rapid detection of PCR amplimers without having to use molecular labels, or surface-fouling agents.

QCM response to solvated, tethered macromolecules.

When the quartz crystal microbalance (QCM) is operated in contact with solution and used to detect inertia increases caused by macromolecules binding to its surface, resonance frequency shifts are reported in the literature to be greater than, less than, and the same as an identical macromolecular mass would cause as a dry layer. A previous report of wet and dry M13 DNA giving the same, linear frequency versus mass response is examined. The M13 data are shown to follow the reciprocal of the square root of mass, not the reported linear relationship. New experiments on RNA duplexes oscillated in solution are reported. A lossy polymer layer is placed between the QCM and RNA. When changes in density, viscosity, and included water are eliminated, the response remains linear for a constant adlayer thickness. The expectation that response per unit mass should decrease with distance from the QCM surface is demonstrated. Total decoupling of mass lying beyond the acoustic overlayer is also demonstrated. The present results are placed in context with recently published results from a study of progressively thicker protein layers bound to the QCM.

Detection of poly (U) hybridization using azido modified poly (A) coated piezoelectric crystals.

A technique has been developed which uses AT-cut, 9 MHz piezoelectric crystals for the immobilization of single stranded nucleic acids and the subsequent hybridization reactions. This hybridization technique is based on detecting small changes in mass on the surface of a piezoelectric crystal which occur upon immobilizing azido containing probe nucleic acid on the surface and hybridizing complementary target nucleic acid to previously immobilized probe. The immobilized probe could be used for repeated hybridization tests. The hybridization assays were performed in solution and the frequency measurements were performed in the dry state.

Singlet and triplet reactivity in the photoreduction of oxonine(3,7-diaminophenoxazin-5-ium chloride) by iron (II).

The oxazine dye, oxonine (3,7-diaminophenoxazin-5-ium chloride), 1, is photoreduced by Fe (II) sulfate in dilute sulfuric acid. The reaction mechanism is analogous to that for the photo-reduction of thiazine dyes by Fe (II), the most important difference being that reduction of oxonine occurs predominantly from its excited singlet state, S1, rather than from the triplet state, T1. The latter is formed with an intersystem crossing (isc) quantum yield of ca 1.7 x 10(-3). The quenching of S1 by Fe (II) has a rate constant kSQ = 2.2 +/- 0.1 x 10(9) M-1 s-1 and affords the one electron reduced product, semioxonine (R), with a limiting quantum yield, phi SR, of 0.26 +/- 0.02. In contrast, quenching of T1, generated by bromide ion quenching of S1 or by diacetyl sensitization, occurs with KTQ approximately 1.2 x 10(6) M-1 s-1, extrapolated to zero ionic strength, and affords R with a limiting probability, phi TR = 1.1 +/- 0.2. Three possible reasons for the lower quantum yield of the more exothermic S1 reduction are discussed. These are energy transfer from S1 to Fe (II), different rates of escape of R from the encounter complex as a consequence of the different states of protonation of R as initially formed from S1 and T1, and spin allowed back electron transfer in an exciplex formed between S1 and Fe (II). Evidence is also presented for a very low probability (ca 1%) induced isc from the encounter of S1 with paramagnetic Fe (II). Rate parameters for other processes important to the overall reduction mechanism such as disproportionation of R to leucooxonine L and oxonine, k(R)DIS = 1.7 +/- 0.2 x 10(9) M-1 s-1, oxidation of R by Fe (III), k(R)OX = 1.5 +/- 0.1 x 10(5) M-1 s-1, and oxidation of L by Fe (III), kLOX = 1.1 +/- 0.1 x 10(3) M-1 s-1, have also been measured. These results are contrasted with those for the closely related thionine/Fe(II) photoredox reaction, the most well understood system for photogalvanic energy conversion.