Fluorophores characteristics

Molecular rotors are fluorophores characteristic for having a fluorescent quantum yield that strongly depends on the viscosity of the solvent [50], This property relies on the ability to resume a twisted conformation in the excited state (twisted intramolecular charge transfer or TICT state) that has a lower energy than the planar conformation. The de-excitation from the twisted conformation happens via a non-radiative pathway. Since the formation of the TICT state is favored in viscous solvents or at low temperature, the probability of fluorescence emission is reduced under those conditions [51]. Molecular rotors have been used as viscosity and flow sensors for biological applications [52], Modifications on their structure have introduced new reactivity that might increase the diversity of their use in the future [53] (see Fig. 6.7). 

The approach to standardization used by Haaijman (53) and others (66,67), in which the fluorophor is incorporated within or bound to the surface of a plastic sphere, is more versatile than the use of inorganic ion>doped spheres, since the standard can be tailored exactly to the specifications required by the analyte species. However, this approach increases the uncertainty of the measurement because the photobleaching characteristics of both the standard and the sample must be considered. The ideal approach is to employ both types of standards. The glass microspheres can be used to calibrate instruments and set instrument operating parameters on a day-to-day basis, and the fluorophor-doped polymer materials can be used to determine the concentration-instrument response function. 

The results reported showed that V450 6a is as fluorescent as, or more fluorescent than, the existing fluorophores with similar spectral characteristics (e.g., Pacific Blue 5), whereas two of the three antibody clones tested demonstrated that a 20-30% gain in signal could be obtained by using V450 6a. 

Pyrene fluorophores are also used as probes. Derivatives of pyrene show /.max/ Xem 340/376 nm, e 4.3 x 104 M 1 cm-1, and environmental sensitivity, this fluorophore can be used to report on RNA folding [102]. Pyrene also displays a long-lived excited state (x > 100 ns), which allows for an excited pyrene molecule to associate with a pyrene in the ground state. The resulting eximer exhibits a red-shift in fluorescence intensity (A,em 490 nm). This characteristic can be used to study important biomolecular processes, such as protein conformation [103]. 

Takadate A, Masuda T, Murata C, Tanaka T, Irikura M, Goya S (1995) Fluorescence characteristics of methoxycoumarins as novel fluorophores. Anal Sci 11 97-101... 

As seen from (1) and (2), intermolecular processes may reduce essentially the lifetime and the fluorescence quantum yield. Hence, controlling the changes of these characteristics, we can monitor their occurrence and determine some characteristics of intermolecular reactions. Such processes can involve other particles, when they interact directly with the fluorophore (bimolecular reactions) or participate (as energy acceptors) in deactivation of S) state, owing to nonradiative or radiative energy transfer. Table 1 gives the main known intermolecular reactions and interactions, which can be divided into four groups ... 

Exciplexes are complexes of the excited fluorophore molecule (which can be electron donor or acceptor) with the solvent molecule. Like many bimolecular processes, the formation of excimers and exciplexes are diffusion controlled processes. The fluorescence of these complexes is detected at relatively high concentrations of excited species, so a sufficient number of contacts should occur during the excited state lifetime and, hence, the characteristics of the dual emission depend strongly on the temperature and viscosity of solvents. A well-known example of exciplex is an excited state complex of anthracene and /V,/V-diethylaniline resulting from the transfer of an electron from an amine molecule to an excited anthracene. Molecules of anthracene in toluene fluoresce at 400 nm with contour having vibronic structure. An addition to the same solution of diethylaniline reveals quenching of anthracene accompanied by appearance of a broad, structureless fluorescence band of the exciplex near 500 nm (Fig. 2 )... 

One of the most popular applications of molecular rotors is the quantitative determination of solvent viscosity (for some examples, see references [18, 23-27] and Sect. 5). Viscosity refers to a bulk property, but molecular rotors change their behavior under the influence of the solvent on the molecular scale. Most commonly, the diffusivity of a fluorophore is related to bulk viscosity through the Debye-Stokes-Einstein relationship where the diffusion constant D is inversely proportional to bulk viscosity rj. Established techniques such as fluorescent recovery after photobleaching (FRAP) and fluorescence anisotropy build on the diffusivity of a fluorophore. However, the relationship between diffusivity on a molecular scale and bulk viscosity is always an approximation, because it does not consider molecular-scale effects such as size differences between fluorophore and solvent, electrostatic interactions, hydrogen bond formation, or a possible anisotropy of the environment. Nonetheless, approaches exist to resolve this conflict between bulk viscosity and apparent microviscosity at the molecular scale. Forster and Hoffmann examined some triphenylamine dyes with TICT characteristics. These dyes are characterized by radiationless relaxation from the TICT state. Forster and Hoffmann found a power-law relationship between quantum yield and solvent viscosity both analytically and experimentally [28]. For a quantitative derivation of the power-law relationship, Forster and Hoffmann define the solvent s microfriction k by applying the Debye-Stokes-Einstein diffusion model (2)... 

Day-to-day drifts of instrumental characteristics, differences in temperature and sample preparation may affect the recorded lifetimes. For instance, differences in temperature can affect both the excited state lifetime of the fluorophore and instrument properties like noise or delays of wirings and electronics. 

Figure 4.9 illustrates time-gated imaging of rotational correlation time. Briefly, excitation by linearly polarized radiation will excite fluorophores with dipole components parallel to the excitation polarization axis and so the fluorescence emission will be anisotropically polarized immediately after excitation, with more emission polarized parallel than perpendicular to the polarization axis (r0). Subsequently, however, collisions with solvent molecules will tend to randomize the fluorophore orientations and the emission anistropy will decrease with time (r(t)). The characteristic timescale over which the fluorescence anisotropy decreases can be described (in the simplest case of a spherical molecule) by an exponential decay with a time constant, 6, which is the rotational correlation time and is approximately proportional to the local solvent viscosity and to the size of the fluorophore. Provided that... 

Fluorescence is a process that occurs after excitation of a molecule with light. It involves transitions of the outermost electrons between different electronic states of the molecule, resulting in emission of a photon of lower energy than the previously absorbed photon. This is represented in the Jablonski diagram (see Fig. 6.1). As every molecule has different energy levels, the fluorescent properties vary from one fluorophore to the other. The main characteristics of a fluorescent dye are absorption and emission wavelengths, extinction... 

Many fluorophores are sensitive to changes in the hydropho-bicity of the immediate environment. Therefore, bringing these fluorophores into a different environment may also produce a change in FRET, when a second fluorophore is affected by the emission change of the first. Fluorophores like Nile Red with changes of up to 100 nm when transferred from water to an aprotic organic solvent are principally suitable for such an approach [71], Molecular rotors have the characteristic of having a quantum yield that depends on the viscosity. Such dyes are formed by an electron donor unit and an electron acceptor unit that can rotate relative to each other upon photoexcitation with a behavior that depends on the viscosity of the environment. These dyes have been included in FRET probes for viscosity studies [53],... 

One of the most characteristic features of FRET is its sensitive dependency on the fluorophore distance. This is advantageously used to evaluate structures and conformational changes of peptides, glycopeptides, and proteins among other molecules [164-166], The conformational change of the lipopeptide antibiotic daptomycin from an inactive linear form to a biological active cyclic form... 

Packard, B. Z., Komoriya, A., Toptygin, D. D. and Brand, L. (1997). Structural characteristics of fluorophores that form intramolecular FI-type dimers in a protease substrate. J. Phys. Chem. B 101, 5070-5074. 

The lifetime, therefore, depends not only on the intrinsic properties of the fluorophore but also the characteristics of the environment. For example, any agent that removes energy from the excited state (i.e., dynamic quenching by oxygen) shortens the lifetime of the fluorophore. This general process of increasing the nonradiative decay rates is referred to as quenching. 

Stepping outside of the subject of biochemical protein dynamics there is also a healthy literature on the use of sensing using fluorophores. Spectral and lifetime characteristics of fluorophores are dependent on their environment, for example, pH, O2, and Ca2+, these features are a useful tool, particularly in the study of the basic biology of the cell (see for instance Chapter 4). 

In contrast, time domain instruments attempt to directly measure the decay characteristics of a fluorophore of interest by excitation with ultrashort light pulses and monitoring the decay using either TCSPC [5] or a time gated image intensifier [8],... 

Figure 9.21 The basic structural characteristics of coumarin fluorophores.

BODIPY fluorophores are a class of probes based on the fused, multi-ring structure, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (Figure 9.27) (Invitrogen) (U.S. patent 4,774,339). This fundamental molecule can be modified, particularly at its 1, 3, 5, 7, and 8 carbon positions, to produce new fluorophores with different characteristics. The modifications cause spectral shifts in its excitation and emission wavelengths, and can provide sites for chemical coupling to label biomolecules. 

The spectral characteristics of Lucifer Yellow iodoacetamide produce luminescence at somewhat higher wavelengths than the green luminescence of fluorescein, thus the yellow designation in its name. The excitation maximum for the probe occurs at 426 nm and its emission at 530 nm. The rather large Stoke s shift makes sensitive measurements of emission intensity possible without interference by scattered excitation light. The 2-mercaptoethanol derivative of the fluorophore has an extinction coefficient at pH 7 of about 13,000 M cm-1 at 426nm. 

Antibody molecules can be labeled with any one of more than a dozen different fluorescent probes currently available from commercial sources. Each probe option has its own characteristic spectral signals of excitation (or absorption) and emission (or fluorescence). Many derivatives of these fluorescent probes possess reactive functionalities convenient for covalently linking to antibodies and other molecules. Each of the main fluorophore families contains at least a few different choices in coupling chemistry to direct the modification reaction to selected functional groups on the molecule to be labeled. These choices include amine-reactive, sulfhydryl-reactive, and carbonyl-reactive. Examples of some of the more popular varieties of fluorescent probes can be found in Chapter 9. 

Table 14.1 Characteristics of some fluorophores used for fluorescence microscopy in order of excitation wavelength. A more extended list of fluorophores can be found on the website http //flowcyt.salk.edu/fluo.html...

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