Nanocrystals and Nanoparticles Versus Molecular Fluorescent Labels as Reporters for Bioanalysis and the Life Sciences: A Critical Comparison - Advanced Fluorescence Reporters in Chemistry and Biology - page 9

Table 1 (continued)
Organic dye Semiconductor quantum dot

Binding to
biomolecules

Via functional groups following
established protocols, often binding of
several dyes to single biomolecule,
labeling-induced effects on
spectroscopic properties of reporter
studied for many common dyes

Via ligand chemistry, only few
protocols available, binding
of several biomolecules to
single QD, very little
information on labeling-
induced effects

0.5 nm

Size 1-6 nm

Thermal stability Dependent on dye class, can be critical for
NIR-dyes

High, depends on shell/ligands

Photochemical
stability

Sufficient for many applications (vis), but
can be critical for high-light flux
applications (e.g., fluorescence
microscopy), often problematic for
NIR dyes

High (vis and NIR), orders of
magnitude that of organic
dyes, can reveal
photobrightening

Toxicity From very low to high, dependent on dye Little known yet (heavy metal

leakage to be prevented,
nanotoxicity)

Reproducibility
of labels
(optical,
chemical
properties)

Good, due to defined molecular structure
and established methods of
characterization, available from
commercial sources

Limited by complex structure
and surface chemistry,
limited data available, few
commercial systems
available, often individual
solutions

Single-molecule
capability

Moderate, limited by photobleaching Good, limited by blinking

FRET Well described FRET pairs, mostly single

donor-single acceptor configurations,
enables optimization of reporter
properties

Few examples, single
donor-multiple acceptor
configurations possible,
limitation of FRET efficiency
due to nanometer-size of
QD-coating

Spectral
multiplexing

Possible, 3 colors (MegaStokes dyes), 4
colors (energy-transfer cassettes)

Ideal for multicolor experiments,
up to 5 colors demonstrated

Lifetime
multiplexing

Possible Possible

Signal
amplification

Established techniques Unsuitable for many enzyme-

based techniques, other
techniques remain to be
adapted and/or established

a

FWHM: full width at half height of the maximum
b Dyes with resonant emission like fluoresceins, rhodamines, cyanines (see section 3.3 )
c CT dyes (see section optical properties, organic dyes)
d Spectroscopic data taken from [ 29 - 33 ]; data for Alexa750 provided by Invitrogen

wavelength below the first excitonic absorption band and a comparatively narrow
luminescence band of typically Gaussian shape. Both the onset of absorption and
the spectral position of the emission band shift to higher energies with decreasing
particle size (Table 1 and Fig. 1a-c ). This size dependence is caused by the
alteration of the electronic properties of these materials (e.g., energetic position