Nucleic Acids and Techniques

Analytical techniques that utilise biopolymers, ie, natural macromolecules such as proteias, nucleic acids, and polysaccharides that compose living substances, represent a rapidly expanding field. The number of appHcations is large and thus uses hereia are limited to chiral chromatography, immunology, and biosensors. 

Both the ease of use of this method for characterization of proteins and nucleic acids, and the abiHty to analyze many samples simultaneously for comparative purposes, have led to the prevalence of this technique. The drawbacks of a polyacrylamide matrix is that acrylamide is a neurotoxin, the reagents must be combined extremely carefiiUy, and the gels are not as pHable as most agarose gels. 

Crystallisation. The ultimate in purification of proteins or nucleic acids is crystallisation. This involves very specialised procedures and techniques and is best left to the experts in the field of X-ray crystallography who provide a complete picture of the structure of these large molecules. [A. Ducruix and R. Gieg6 eds. Crystallisation of Nucleic Acids and Proteins A Practical Approach, 2nd Edition, 2000,... 

R. C. Allen and B. Budowle. Gel electrophoresis of proteins and nucleic acids selected techniques. Walter de Gruyter, Berlin (1994). 

Finally, we should note that a particularly important area of application where density functional techniques, in spite of the deficiencies noted above, are virtually without competition is provided by biochemically relevant molecules, such as enzymes or nucleic acids. The techniques discussed in this section are virtually the only quantum chemical methods which can be applied in this context due to their outstanding price/performance ratio. For example, the 13C and 15N chemical shifts in bacteriochlorophyll A have been studied by Facelli, 1998, and in another investigation the 57Fe, 13C and 170 shifts in iron porphyrin derivatives gave important clues as to the structural details of these species, as shown by McMahon et al 1998. 

Recent developments in drug discovery and drug development spurred the need for novel analytical techniques and methods. In the last decade, the biopharmaceutical industry set the pace for this demand. The nature of the industry required that novel techniques should be simple, easily applicable, and of high resolution and sensitivity. It was also required that the techniques give information about the composition, structure, purity, and stability of drug candidates. Biopharmaceuticals represent a wide variety of chemically different compounds, including small organic molecules, nucleic acids and their derivatives, and peptides and proteins. 

In general, the mechanism of heat and alkaline solution for DNA extraction may be based upon a hypothesis, previously proposed for the AR technique.32 Strong alkaline solution may denature and hydrolyze proteins, resulting in breaking cell and nuclear membranes as well as disrupting cross-linkages due to formalin fixation. It is no surprise to observe the similarity between retrieval of nucleic acid and retrieval of protein (antigen) based on a similar chemical reaction of formaldehyde with these two kinds of macromolecules (Fig. 3.1).15"19... 

Montone KT, Brigati DJ, Budgeon LR. Anatomic viral detection is automated the application of a robotic molecular pathology system for the detection of DNA viruses in anatomic pathology substrates, using immunocytochemical and nucleic acid hybridization techniques. Yale J. Biol. Med. 1989 62 141-158. 

Fluorescent labels, by contrast, can provide tremendous sensitivity due to their property of discrete emission of light upon excitation. Proteins, nucleic acids, and other molecules can be labeled with fluorescent probes to provide highly receptive reagents for numerous in vitro assay procedures. For instance, fluorescently tagged antibodies can be used to probe cells and tissues for the presence of particular antigens, and then detected through the use of fluorescence microscopy techniques. Since each probe has its own fluorescence emission character, more... 

Alternative methods of diagnosis include enzyme immunoassay, DNA probes, and nucleic acid amplification techniques. 

Shadowcasting protocols for electron microscopy can be found in Glenny (56), Coggins (57), and Slayter (53). The two former references concern proteins and nucleic acids, and the latter reference is dedicated to a comprehensive application of the technique. 

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

Electrophoresis has been applied for decades in analytical chemistry. It is still the method of choice for the determination of proteins and nucleic acids. The technique of CE is classified in three main groups of methods [1] ... 

---