Nucleic acids, fixative compounds

In commercial fixed wavelength UV detectors, Xmax is often set at 254 nm. This specific wavelength will provide a wide range of applications, giving strong absorption bands for biologically important compounds such as amino acids, proteins, enzymes and nucleic acid constituents. 

Figure 12.4 In the presence of formaldehyde, the exocyclic nitrogen (encircled, upper left) on a nucleotide forms an Af-hydroxymethyl adduct (upper center). Further denaturing reactions of formalin-fixed nucleic acids during tissue processing lead to a compound ethoxymethyl adduct (lower right), fragments from depurination (lower left), cross-hnks to associated proteins (not shown), and hydrolysis of phosphodiester bonds (not shown).

Other fluorogenic dyes, such as DAPI, ethidium bromide and the cyanine dyes, bind to DNA and/or RNA and undergo changes in fluorescence intensity of up to 1000-fold. Depending on the probe, these compounds can be used to image fixed cells or track mitotic events. Combinations of probes with different specificities for single-stranded, double-stranded and ribosomal RNA have been used to characterize the quantity and conformation of nucleic acids throughout the cell cycle. 

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