Chemical derivatization probes

Regardless of the type of enzymatic labeling used, it is important that the label be incorporated into the nucleoside triphosphates or primers in a way that does not affect enzyme recognition and activity. Thus, every enzymatic labeling procedure for modifying RNA or DNA probes must start with chemical derivatization of individual nucleotides. Of the many chemical procedures that can be used to modify a nucleoside triphosphate monomer, there are only a few that will result in a derivative still able to be enzymatically added to an existing oligonucleotide strand. 

Fluorescent probes containing sulfhydryl-reactive groups can be coupled to DNA molecules containing thiol modification sites. The chemical derivatization methods outlined in Section 2.2 (this chapter) may be used to thiolate the oligo for subsequent modification with a fluorophore. Appropriate fluorescent compounds and their reaction conditions may be found in Chapter 9. The protocol discussed in the previous section can be used as a general guide for labeling DNA molecules. 

Another AFM-based technique is chemical force microscopy (CFM) (Friedsam et al. 2004 Noy et al. 2003 Ortiz and Hadziioaimou 1999), where the AFM tip is functionalized with specific chemicals of interest, such as proteins or other food biopolymers, and can be used to probe the intermolecular interactions between food components. CFM combines chemical discrimination with the high spatial resolution of AFM by exploiting the forces between chemically derivatized AFM tips and the surface. The key interactions involved in food components include fundamental interactions such as van der Waals force, hydrogen bonding, electrostatic force, and elastic force arising from conformation entropy, and so on. (Dther interactions such as chemical bonding, depletion potential, capillary force, hydration force, hydrophobic/ hydrophobic force and osmotic pressure will also participate to affect the physical properties and phase behaviors of multicomponent food systems. Direct measurements of these inter- and intramolecular forces are of great interest because such forces dominate the behavior of different food systems. 

To modify the unique chemical groups on nucleic acids, novel methods have been developed that allow derivatization through discrete sites on the available bases, sugars, or phosphate groups (see Chapter 1, Section 3 for a discussion of RNA and DNA structure). These chemical methods can be used to add a functional group or a label to an individual nucleotide or to one or more sites in oligonucleotide probes or full-sized DNA or RNA polymers. 

In some manufacturing process analysis applications the analyte requires sample preparation (dilution, derivatization, etc.) to afford a suitable analytical method. Derivatization, emission enhancement, and other extrinsic fluorescent approaches described previously are examples of such methods. On-line methods, in particular those requiring chemical reaction, are often reserved for unique cases where other PAT techniques (e.g., UV-vis, NIR, etc.) are insufficient (e.g., very low concentrations) and real-time process control is imperative. That is, there are several complexities to address with these types of on-line solutions to realize a robust process analysis method such as post reaction cleanup, filtering of reaction byproducts, etc. Nevertheless, real-time sample preparation is achieved via an on-line sample conditioning system. These systems can also address harsh process stream conditions (flow, pressure, temperature, etc.) that are either not appropriate for the desired measurement accuracy or precision or the mechanical limitations of the inline insertion probe or flow cell. This section summarizes some of the common LIF monitoring applications across various sectors. 

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