Communications
or genetically modified cells to be active.[20,21] To our knowl-
edge there are no examples to date of multicolor quenched
probe sets selective for different caspases.
tion wavelength for probe 1 is 380 nm. All three sensors can
be excited using one excitation filter (330–380 nm) under an
epifluorescence microscope.
Here we describe the synthesis, fluorescence, and enzyme
substrate properties of a set of three multicolor caspase
chemosensors built with distinct ODF labels. This novel
DNA-peptide conjugate sensor design utilizes different ODF
sequences as fluorophores and dabcyl as a general quencher,
and it contains short caspase substrate peptides in between.
We demonstrate selective reporting of three different cas-
pases by distinct color responses. Further, an ODF caspase
probe is shown to function in cell culture to report on
apoptosis.
Absorption spectra were obtained both for the chemo-
sensors and for the ODF components. The spectra of the
ODF sensors show the expected bands that are characteristic
of the dye components (Figure S1). Bands are visible for
pyrene, perylene, and monomer K; in addition, the long-
wavelength absorption band of the dabcyl (methyl red)
quencher is also present. To test the inherent quenching
efficiency of dabcyl for the three ODF sequences, we
separately prepared dabcyl-quenched conjugates with a
previously reported ester linkage rather than amide link-
ages.[9] These model compounds allowed all three fluoro-
phore–quencher pairs to be completely released by one
enzyme under identical conditions. Experiments showed that
the YYYY sequence has the highest fluorescence turn-on
ratio, about 60-fold at 480 nm.[9] EE and YKY also showed
strong fluorescence turn-on, ca. 20-fold at the long-wave-
length emission bands (Figure S2). The liberated ODFs
appeared cyan, yellow-white, and red under a UV lamp
after the cleavage reactions were complete (Figure S2). These
results indicate that a simple dabcyl group can be used to
quench all tested multiply colored ODFs with good quench-
ing efficiency, thus significantly reducing the complexity of
fluorophore–quencher pair selection in chemosensor design.
For the three peptide-linked caspase probes (1–3) in this
study, spectral comparison before and after cleavage can be
made indirectly, by comparing residual emission spectra of
the unreacted (dark) probes with the spectra of the corre-
sponding ODF fluorophores alone. Results (Figure S3) are
similar to the ester-linked model systems, showing (for the
unreacted probes) strong quenching at the long-wavelength
bands.
Next we turned to the enzymatic reporting potential of
caspase substrate probe compounds 1–3. Homogeneous
enzymatic assays for the three candidate chemosensors were
performed with recombinant human caspases 2, 7, and 9,
respectively, in 10 mm HEPES buffer (pH 7.3). Results
showed that significant fluorescence enhancement was
observed in each case (Figures 1 and S4), indicating the
occurrence of a measurable degree of peptide cleavage over
the 4 h time course. The probes 1–3 yielded fluorescence
enhancements at 550, 480, and 620 nm respectively, consistent
with the results of the above model studies. The reaction rates
were lower than for the esterase references, particularly for
probe 3 which yielded a relatively small 76% enhancement
after 4 h. We expect that the rates of caspase cleavage can be
affected by multiple factors, including inherent enzyme
activity, instability of the enzymes over the assay period,
and possibly unfavorable interactions between ODFs and the
caspase active sites.
Each caspase chemosensor contains three parts: an ODF
sequence as the fluorophore, a quencher, and a short peptide
as the caspase substrate in the middle (Scheme 1). We
employed
a
convergent strategy for their synthesis
(Scheme S1, Supporting Information). First, three ODF
Scheme 1. Structures of ODF-based fluorescent caspase chemosensors
and their components. A) Complete structure of an ODF sensor
(probe 1 is shown as an example); B) Structures of monomers
incorporated into ODF labels; C) Sequences of the three probes
designed for caspases 2, 7, and 9, respectively.
sequences with different emission colors were prepared on a
DNA synthesizer: EE (yellow), YYYY (cyan), and YKY
(orange). Two C3 spacers (S, with one phosphate group each)
were placed at the 3’ end of each ODF sequence to improve
the solubility in water, and an azide group was placed at the 5’
end for bioorthogonal conjugation by “click” cycloaddition.[9]
Three short caspase substrate peptides were synthesized:
Val-Asp-Val-Ala-Asp for caspase-2, Asp-Glu-Val-Asp for
caspase-3/7, and Leu-Glu-His-Asp for caspase-9.[22–25] 5-Hex-
ynoic acid was coupled to the N-terminus of each peptide to
provide an alkyne for conjugation, and dabcyl was coupled to
the C-termini as a prospective general quencher.
Three caspase chemosensors with peptide–DNA conju-
gate structure were synthesized (see sequences in Figure 1c):
probe 1 for caspase-2, probe 2 for caspase-7, and probe 3 for
caspase-9. The compounds were purified by HPLC, and
identities were confirmed by MALDI-MS and by spectral
characterization. The absorption spectra indicate that probes
2 and 3 can be excited at 340 nm. Because perylene (E) does
not have strong absorbance at 340 nm, the optimum excita-
To test whether the probes exhibited selectivity for one
caspase over another, assays were performed using an
equimolar mixture of the three probes. One caspase was
added into a cocktail containing equal amounts of all three
caspase chemosensors, and the reaction mixture was incu-
bated at 308C for 4 h. Fluorescence changes were analyzed by
emission spectra (Figure 2) and visual inspection (Figures 2G
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Angew. Chem. Int. Ed. 2011, 50, 5105 –5109