Fluorescence chain reaction

The use of agarose as an electrophoretic method is widespread (32—35). An example of its use is in the evaluation and typing of DNA both in forensics (see Forensic chemistry) and to study heritable diseases (36). Agarose electrophoresis is combined with other analytical tools such as Southern blotting, polymerase chain reaction, and fluorescence. The advantages of agarose electrophoresis are that it requires no additives or cross-linkers for polymerization, it is not hazardous, low concentration gels are relatively sturdy, it is inexpensive, and it can be combined with many other analytical methods. 

Quantitative polymerase chain reaction, also called real-time RT-PCR or QPCR, is a method which employs insertion of a signal, such as fluorescence or enzyme activity, into PCR products generated by RT-PCR to determine the amount of messenger RNA (mRNA) in a tissue accurately. 

Rigler, R., Foldes-Papp, Z., Meyer-Almes, F. J., Sammet, C., Volcker, M. and Schnetz, A. (1998). Fluorescence cross-correlation A new concept for polymerase chain reaction. J. Biotechnol. 63, 97-109. 

Numerous autoxidation reactions of aliphatic and araliphatic hydrocarbons, ketones, and esters have been found to be accompanied by chemiluminescence (for reviews see D, p. 19 14>) generally of low intensity and quantum yield. This weak chemiluminescence can be measured by means of modern equipment, especially when fluorescers are used to transform the electronic excitation energy of the triplet carbonyl compounds formed as primary reaction products. It is therefore possible to use it for analytical purposes 35>, e.g. to measure the efficiency of inhibitors as well as initiators in autoxidation of polymer hydrocarbons 14), and in mechanistic studies of radical chain reactions. 

The rather stable diacyl peroxides such as dibenzoyl or phthaloyl peroxide have attracted special interest as some of their reactions, mostly not chain reactions, are chemiluminescent. Triplet-singlet energy transfer is very often involved, and emission generally occurs only when a fluorescer is present since the primary excited products cannot emit in the visible range of the spectrum. 

Naphthalene-2,3-dicarboxaldehyde Nicotinamide adenine dinucleotide N-Acetylneuraminic acid 4-Fluoro-7-nitrobenzoxadiazole Naphthalene-2,3-dicarboxaldehyde Nondestructive readout Near infrared Near infrared fluorescence Nuclear magnetic resonance 2-Nitrophenyl oxalate 1,1 -Oxalyldiimidazole Polycyclic aromatic hydrocarbon Principal component analysis Photosensitized chemiluminescence Pentachlorophenyl oxalate Polymerase chain reaction... 

Rapid antigen and point-of-care tests, direct fluorescence antibody test, and the reverse-transcription polymerase chain reaction assay may be used for rapid detection of virus. 

The RNA molecules, ribosomal RNA (rRNA) and messenger RNA (mRNA) play key roles in the protein synthesis. The amount of RNA in individual cells or in a community may, therefore, be taken as an indicator of protein synthesis and, thus, microbial activity. The number of active cells can be detected by fluorescent in situ hybridization (FISH) (Amann et al. 1995). By this method, individual cells carrying high concentrations of rRNA, situated on ribosomes, are quantified by fluorescence microscopy. The amount of rRNA in a community can also be detected by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), where rRNA extracted from soil is detected by creating a DNA copy and separating by gel electrophoresis (Duineveld et al. 2001). 

Abbreviation Bp, nucleotide base pairs cDNA, complementary DNA ChIP, chromatin Immunoprecipi-tation Cy5, cyanine 5-dCTP Cy3, cyanine 3-dCTP ESTs, expressed sequence tags FDR, false discovery rate MIAME, minimum information about a microarray experiment mRNA, RNA, messenger NIA, National Institutes of Aging RFUs, relative fluorescence units RT-PCR, reverse transcriptase polymerase chain reaction SAGE, serial analysis of gene expression SAM, significance analysis of microarrays... 

If ki and k.i are much larger than kj, the reaction Is controlled by kj. If however, ki and k.i are larger than or comparable to kz, the reaction rate becomes controlled by the translational diffusion determining the probability of collisions which Is typical for specific diffusion control. The latter case Is operative for fast reactions like fluorescence quenching or free-radical chain reactions. The acceleration of free-radical polymerization due to the diffusion-controlled termination by recombination of macroradicals (Trommsdorff effect) can serve as an example. 

FLUORESCENCE PROPAGATION CHAIN REACTION CHAIN TRANSFER INITIATION TERMINATION Propanal, synthesis of,... 

The initiation step can be photoinduced. If a bottle is sitting in sunlight, UV photons (fluorescent lights are also more dangerous than incandescent lights) can cause photodissociation to initiate the chain reaction much faster than in the dark. [Guess why many chemicals are sold in brown bottles ]... 

Analysis of polymerase chain reaction-product by capillary electrophoresis with laser-induced fluorescence detection and its application to the diagnosis of medium-chain acyl-coenzyme A dehydrogenase deficiency. 

A thermal cycler (see 8.2.3.2 Polymerase Chain Reaction) is required for the cycle sequencing reaction. For fluorescent cycle sequencing we recommend instruments from Applied Biosystems (e.g. the 16-capillary ABI PRISM 3100 Genetic Analyser) other instruments are available from GC Healthcare and Beckman. For detailed instructions, refer to the respective user s manual or chemistry guide. 

Another class of readout measures RNA expression levels, with the three most common methods being chip-based hybridization/fluorescence techniques, realtime polymerase chain reaction (RT-PCR) and quantitative nuclease protection assays (QNPA) [48, 49]. Chip-based methods are widely used for whole-genome scans (discussed in more detail below), but have a disadvantage that they are relatively expensive and so are not really high throughput. The quantitative reproducibility and dynamic range of these chip-based methods are also lower than for the other RNA readout techniques. RT-PCR is a more quantitative technique for measuring transcript levels, and is typically run for up to 40 transcripts at a time. QNPA is another... 

We use the same reactor geometry for photochlorinations because, given the high quantum yields of these chain reactions, irradiance must not be optimized to achieve good productivity. These reactors may then be equipped with fluorescent tubes for which no external cooling and no water filters are needed. 

---