The cyanine dyes also show important differences in some physical characteristics-particularly in cell membrane permeability and nucleic acid specificity-that allow their distribution into distinct classes, and these classes are discussed in detail below and in the following sections of this chapter. Their fluorescence absorption and emission spectra span the visible-light spectrum from blue to near-infrared ( Figure 8.1.2) with additional absorption peaks in the UV, making them compatible with many different types of instrumentation. Moderate to very high affinity for nucleic acids, with little or no staining of other biopolymers.Large fluorescence enhancements (often over 1000-fold) upon binding to nucleic acids, with increases in quantum yields to as high as 0.9.Very low intrinsic fluorescence, with quantum yields usually less than 0.01 when not bound to nucleic acids.High molar absorptivity, with extinction coefficients typically greater than 50,000 cm -1M -1 at visible wavelengths.Molecular Probes nucleic acid–binding cyanine dyes share several important spectroscopic and physical properties: Other nucleic acid stains, including acridine orange, 7-AAD, LDS 751 and hydroxystilbamidine.Minor-groove binders ( Figure 8.1.1), such as DAPI and the Hoechst dyes.Intercalating dyes ( Figure 8.1.1), such as ethidium bromide and propidium iodide.
The three classes of classic nucleic acid stains ( Properties of classic nucleic acid stains-Table 8.4) include: Amine-reactive SYBR dye that can be used to form bioconjugates.Cell-permeant SYTO™ family of dyes ( Cell-permeant cyanine nucleic acid stains-Table 8.3).Cell-impermeant TOTO™, TO-PRO™ and SYTOX™ families of dyes ( Cell membrane–impermeant cyanine nucleic acid stains-Table 8.2).Premier dyes for ultrasensitive nucleic acid quantitation and gel staining ( Specialty nucleic acid reagents for molecular biology-Table 8.1).
The four classes of Invitrogen™ Molecular Probes™ cyanine dyes include: The sections that follow describe applications of these nucleic acid stains for genomics research. This section discusses the physical properties of the various classes of dyes listed below. We offer an extensive assortment of nucleic acid stains, many of which have been developed in our research laboratories.