Chapter 4 - Cyanine dyes as fluorescent non-covalent labels for nucleic acid research

Abstract

The applications of cyanine dyes as nucleic acid probes in the field of biotechnology are numerous and continuously expanding. Among the most numerous applications of cyanine dyes is the visuazation of DNA by following different biological processes and quantification of DNA in solution. YOYO-1-labeled complexes may be employed as qualitative DNA markers in intracellular delivery studies. With the combination of a green-fluorescent SYTO 9 dye and red-fluorescent hexidium iodide, it is possible to perform a fluorescent assay for gram reaction. When mixed populations of live gram-negative and gram-positive bacteria are simultaneously stained with the membrane permeable SYTO 9 dye in combination with hexidium iodide, the gram-negative bacteria fluoresce green and the gram-positive bacteria fluoresce red-orange. Dead bacteria do not exhibit predictable staining patterns. Generally, all intercalating cyanine dyes are suitable for polymerase chain reaction (PCR) if they are added after the completion of the reaction, thus giving a fluorescence signal. The best methods for quantitative PCR are commonly known as realtime PCR because one can monitor the product accumulation during the reaction, rather than merely assaying it at the end. The most used dye for real-time PCR is SYBR Green I (SG).