Proteins nucleic acid-protein cross-links

Table 8.3 Nucleobases bearing photosensitizer groups commonly used for nucleic acid/protein cross-linking studies [51,53].

Metabolically, formaldehyde is rapidly oxidized to formic acid (see Section 14.7), which is responsible in large part for its toxicity. Formaldehyde reacts by addition and condensation reactions with a variety of biocompounds, including DNA and proteins, and in so doing forms adducts and DNA-protein cross-links.9 Formaldehyde is incorporated into proteins and nucleic acids as the -CH3 group. Reactive formaldehyde has a short systemic lifetime of only about 1 min its formic acid metabolic product has a longer metabolic lifetime. 

Fixation in formalin is suitable because the induced protein-protein and protein-nucleic acid cross-links preserve the tissue efficiently while retaining morphology relatively intact. However, the macromolecular network introduced by formalin significantly reduces the access of FISH probes to target DNA. Consequently, the initial steps in a FISH staining must address suitable breakdown of this network. 

Steen, H. and Jensen, O.N. (2002) Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry. Mass Spectrom. Rev., 21 (3), 163-182. 

Sephadex is one of the most popular materials for gel chromatography. It is widely used by biochemists for separating proteins, nucleic acids, enzymes, and carbohydrates. Most often, water or aqueous solutions of buffers are used as the moving phase. Chemically, Sephadex is a polymeric carbohydrate that has been cross-linked. The degree of cross-linking determines the size of the "holes" in the polymer matrix. In addition, the hydroxyl groups on the polymer can adsorb water, which causes the material to swell. As it expands, "holes" are created in the matrix. Several different gels are available from manufacturers, each with its own set of characteristics. 

Sephadex. Other carbohydrate matrices such as Sephadex (based on dextran) have more uniform particle sizes. Their advantages over the celluloses include faster and more reproducible flow rates and they can be used directly without removal of fines . Sephadex, which can also be obtained in a variety of ion-exchange forms (see Table 15) consists of beads of a cross-linked dextran gel which swells in water and aqueous salt solutions. The smaller the bead size, the higher the resolution that is possible but the slower the flow rate. Typical applications of Sephadex gels are the fractionation of mixtures of polypeptides, proteins, nucleic acids, polysaccharides and for desalting solutions. 

Sonenberg, N. (1981). ATP/Mg++-dependent cross-linking of cap binding proteins to the 5 end of eukaryotic mRNA. Nucleic Acids Res. 9, 1643—1656. 

Ion-exchange resins are cross-linked polymers which are typically polystyrene, cellulose or agarose based. Polystyrene is hydrophobic in nature and useful for inorganic ions and small molecules while cellulose and agarose are hydrophilic and more useful for the larger, biologically important molecules, e.g. proteins and nucleic acids, which either would be adversely affected by a hydrophobic environment or could not gain access to the small pore structure. 

There is some suggestive evidence that exposure to ozone accelerates the aging process(es). Bjorksten and Bjorksten and Andrews have presented evidence that aging is due to irreversible cross-linking between macromolecules, principally proteins and nucleic acids. Aldehydes were included in the list of cross-linking agents, and these can be produced in the lung as a result of ozone exposure. ... 

---