Probe labeled

Fig. 6.5 Schematic representation of a bioelectronic protocol for detection of DNA hybridization (A) binding of the target to magnetic beads (B) hybridization with CdS-labeled probe (C) dissolution of CdS tag (D) potentiometric stripping detection at a mercury-film electrode. (Reprinted from [136], Copyright 2009, with permission from Elsevier)...

Alkaline phosphatase-labeled probes are synthesized so that 18 bases are complementary to sequences on the arms of the bDNA. Three hybridization sites are located on each branch for a total binding capacity of 45 labeled probes per bDNA molecule. The alkaline phosphatase catalyzes the dephosphorylation of chemiluminescent substrate, dioxetane (Lumi-Phos Plus, Lumigen, Detroit, MI). The intensity of the light emission is measured with a plate luminometer as relative luminescent units. 

The molecular sensitivities of the first and second generations of the bDNA assays were limited by nonspecific hybridization between the amplification probes and other nucleic acids. Short regions of hybridization between any of the probes constituting the amplification system, (preamplifier, amplifier, and labeled probe) and any nontarget nucleic acid sequence leads to amplification of the background signal. Capture probes, capture extenders, and sample nucleic acid are all sources of this background hybridization (Collins et al 1997). 

The level of HBV DNA in serum or plasma probably better reflects the replicative activity of HBV. Several assays for the quantitation of HBV DNA are commercially available. In the Genostics assay (Abbott Laboratories), an, 25I-labeled probe binds to single-stranded HBV DNA in solution, followed by separation of free probe and hybrids using Sepharose chromatography (Kuhn et al., 1988). The... 

Indeed, a bDNA assay for diagnosis of African trypanosomiasis was developed and compared with buffy coat microscopy for detection of T brucei in human blood samples (Harris etal., 1996). Two repetitive DNA sequences found only in the T. brucei complex, a 177-bp satellite repeat and the ribosomal mobile element, were selected as targets in the bDNA assay. The assay used the standard bDNA components capture probes, target probes, amplifier molecules, and alkaline phosphatase-labeled probes. Various blood fractions and sample preparation methods were examined. Ultimately, buffy coat samples resulted in the highest sensitivity. Although typanosomes do not infect leukocytes, they cosediment with them. 

Hyde, J. S. and W. K. Subczynski. 1984. Simulation of ESR spectra of the oxygen-sensitive spin-label probe CTPO. J. Magn. Reson. 56 125-130. 

Wu XL, Tian M, Fie HZ et al (2009) Synthesis and biological applications of two novel fluorescent proteins-labeling probes. Bioorg Med Chem Lett 19 2957-2959... 

A Petri dish containing bacterial colonies is blotted with nitrocellulose paper. This transfers a large portion of each colony to the paper, which is saturated with a solution that lyses (breaks open) the cells. The DNA of the lysed colonies is denatured with alkali. The nitrocellulose paper is neutralized, washed, and the paper either baked in an oven or treated with ultraviolet light to immobilize the denatured DNA. The DNA on the paper is hybridized with the labeled probe of interest, and the excess label is washed off. The dried paper is exposed to photographic film and the film developed. The exposed spots on the film can be matched with the colonies on the master plate and colonies picked off for further study. 

A review of the application of ESR to the study of free radical polymerisation is given by Yamada and co-workers [146]. A survey of the application ESR spectroscopy spin label/probe methods in heterogeneous polymer systems is provided by Veksli and co-workers [147]. Spin probe methods allow the study of the MD of the polymer, its free volume, phase separation and phase morphology. 

Incubate >1 /ig of RNA with a 3- to 10-fold molar excess of radio-labeled probe (about 150 to 600 pg per 10 /ig total RNA) in hybridization buffer. 

Place a microarray slide in a hybridization chamber and pipette 25 Ail of the labeled probe mixture on the slide surface near one end of the microarray print area. 

TRITC has been used in numerous applications involving fluorescence detection, including double-staining techniques with fluorescein-labeled probes (Mossberg and Ericsson, 1990), the synthesis of fluorescently labeled DNA probes (Smith et al., 1985), as a label in homogeneous... 

Preparation of a series of phycobiliprotein tandem dyes allows multiplexed analysis of different targets in a sample. In addition, since RPE can be excited by the argon-ion laser at 488 nm, a fluorescein-labeled probe can be used concurrently with RPE alone and RPE-tandem conjugates to create a multiplexed system of different fluorescent probes that can be used simultaneously. Table 9.3 shows the different combinations of dyes that can be used in this type of assay with RPE and APC. 

Purify the labeled probe by ethanol precipitation according to steps 4-7 of the protocol previously described for nick translation. 

Isolate the labeled probe by alcohol precipitation as described previously for nick translation. 

Enzymes useful for detection purposes in ELISA techniques (Chapter 26) also can be employed in the creation of highly sensitive DNA probes for hybridization assays. The attached enzyme molecule provides detectability for the oligonucleotide through turnover of substrates that can produce chromogenic or fluorescent products. Enzyme-based hybridization assays are perhaps the most common method of nonradioactive detection used in nucleic acid chemistry today. The sensitivity of enzyme-labeled probes can approach or equal that of radiolabeled nucleic acids, thus eliminating the need for radioactivity in most assay systems. 

Chetrit, P., Gaudin, V., de Courcel, A., and Vedel, F. (1989) A cross-hybridization method for DNA mapping with photobiotin-labeled probes. Anal. Biochem. 178, 273-275. 

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