Probing biochemical reactions

Flow-through sensors integrating detection and a chemical or biochemical reaction rely on immobilization in the probe proper or the flow-cell (or a special housing included in it) of a species intended to take part in or catalyse the reaction by which the analyte, viz. the catalyst or reagent, is measured, according to which the sensors described in this Chapter are divided into two broad categories. 

X-ray absorption spectroscopy is an exciting new tool, ideally suited to probing the immediate environment of a specific atom type in a physical, chemical or biological system. The advent of synchrotron radiation has transformed this technique from a topic of relatively minor interest to one of major scientific importance and activity " . A major attraction of the technique is the possibility it provides of probing a reaction centre in a wide range of materials ranging from an industrial catalyst to an enzyme the technique is not limited by the physical state of the sample. In this review, suitability of this technique for biochemical systems is discussed. 

Peters. K.S. and G.J. Snyder, Time-Resolved Photoacoustic Calorimetry Probing the Energetics and Dynamics of Fast Chemical and Biochemical Reactions, Science. 1053 (August 26, 1988). 

In order to probe chemical constituents and follow their biochemical reaction in cells and tissues, there is a need to make fluorescent labels more specific, brighter, and more robust. This will require greater understanding of the photophysics and photochemistry of fluorescent probes and the mechanisms of their photobleaching. 

The lanthanides and divalent calcium are similar in size and have a tendency for high coordination numbers and these similarities make lanthanide ions as structural probes in biochemical reactions in place of calcium. Further, lanthanide ions can be used as markers... 

In the last two decades there has been a substantial progress in understanding the nature and reactions of biologically relevant free radicals, and the development of new antioxidants. Both biochemical methods and free radical scavenging techniques have been widely employed. Fast reaction kinetic techniques have been found to be very useful in directly probing the reactions of antioxidants with free... 

Donor-acceptor probes are very useful as fluorescent lables in biochemical assay and sensing based on the fluorescence quenching mechanisms. In a closed state form where the donor and acceptor are close to each other, the fluorescence of the donor (reporter) is highly quenched. In an open state, where the donor and receptor are spaced away from each other due to biochemical reactions, the donor fluorescnece is restored. The changes of the fluorescence intensity of the reporter has been used for DNA detection, immunoassay, enzyme sensing and detection of many other bimolecules. 

Weisgraber KH, Newhouse YM, Mahley RW. Apolipoprotein E genotyping using the polymerase chain reaction and allele-specific oligonucleotide probes. Biochem Biophys Res Commun 1988 157 1212-17. 

A somewhat different but mechanistically related reaction is the [2 -f 3] cycloaddition of a functionalized alkyne or nitrile to an azide to form a disubstituted triazole (120) or tetrazole ring (121, 122), linking the respective functionalities irreversibly (Scheme 14b). This click chemistry was used by Sharpless and co-workers (120) in 2001 as a tool to probe biochemical catalysis and substrate activation. The ease of the Cu(I)-catalyzed reaction has created a true explosion (120-160) of simple coupling-functionalization chemistry of all types of biochemical components (sugars, DNA, proteins, enzymes, substrates, inhibitors) (131, 135, 136, 139, 142, 155, 157-160), polymers (126, 134, 140, 147, 154),... 

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