Red light-triggered photoreduction on a nucleic acid template

Article abstract of DOI:10.1039/d0cc03086d

Conjugate Sn(iv)(pyropheophorbide a)dichloride-(peptide nucleic acid) catalyzes reduction of azobenzene derivatives in the presence of complementary nucleic acid (NA) upon irridiation with red light (660 nm). This is the first red light-induced NA-templat

Full text of DOI:10.1039/d0cc03086d

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Red light-triggered photoreduction on a nucleic acid template
Subrata Dutta,a Jennifer Rühler,a Margot Schikora,a† Nina Deussner-Helfmann,b Mike Heilemann,b
Timofei Zatsepin,c,d Patrick Duchstein,e Dirk Zahn,e Günther Knörf and Andriy Mokhira
Received 00th January 20xx,
Accepted 00th January 20xx
DOI: 10.1039/x0xx00000x
Conjugate Sn(IV)(pyropheophorbide)dichloride~(peptide nucleic that is triggered by 532 nm-light,12,13 and (c) oxidation of organic
acid) catalyzes reduction of azobenzene derivatives in the presence substrates mediated by singlet oxygen (1O2).14-17 The latter
of complementary nucleic acid (NA) upon irridiation with red light reaction is photosensitizer (PS) dependent. For example, we
(660 nm). This is the first red light-induced NA-templated have demonstrated that In(pyropheophorbide-a)chloride
photoreduction. It is highly sensitive to single mismatches in the ([In(P~OH)Cl], Scheme 1) is an efficient catalyst, whose activity
NA-template and can detect down to 5 nM NAs.
can be triggered by ~650 nm light. The 1O2-mediated chemistry
has an intrinsic drawback of generating a toxic mediator O2.
1
Due to its rather long lifetime of 3-4 µs in aqueous solution,18,19
1O2 can migrate >100 nm thereby damaging biomolecules. A
solution of this problem could be in using a mediator with a
shorter lifetime, e.g. a photochemically generated electron.
Templated reactions mediated by electron transfer have been
developed by Winssinger group.7-11 These are catalyzed
exclusively by a [Ru(bpy)2phen], which is excited by 455 nm
light. The latter trigger is still toxic to cells,4-6 that can limit
applications of these reactions.
In this paper we describe the first red light-triggered NA-
templated photoreduction (Scheme 1A). We selected
[In(P~OH)Cl] and [Sn(P~OH)Cl2] (Scheme 1B) as possible
photocatalysts based on the following considerations.
Pyropheophorbide a (PH2~OH) is an accessible chlorin derived
from chlorophyll. It has a strong absorbance band in the spectral
region between 600 and 700 nm. Chlorophyll metabolites are
known to catalyse photoreduction of organic compounds, e.g.
ubiquinone in blood plasma.20 Moreover, chlorophylls linked to
a CO2-reducing complex catalyse photoreduction of CO2.21
PH2~OH as well as its known Mg(II) and Zn(II) complexes are
photounstable, whereas its Pd(II) and Pt(II) complexes
Templated reactions are applied for detection of NAs in various
bioanalytical assays.1 Photochemical reactions of this type have
an advantage of the possibility of temporal and spatial
control.2,3 Numerous UV-light driven reactions are known.1-3
However, their usefulness is limited by the toxicity of UV-light
to cells.4-6 This issue stimulated the research towards
development of systems sensitive to visible light. Important
known examples include (a) photoreduction of organic azides
and N-alkylpyridinium salts mediated by a [Ru(bpy)2phen] in the
presence of reducing agents triggered by 455 nm-light,7-11 (b)
Cy3-sensitized oxidation of radical species derived from dyes
a.Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-
Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany.
b.Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-
University, 60438 Frankfurt, Germany.
c. Skolkovo Institute of Science and Technology, Moscow, 126046, Russia.
d.Chemistry Department, M.V.Lomonosov Moscow State University, Leninskie gory,
1-3,Moscow 119992, Russia.
e. Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-
Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany
f. Johannes Kepler University Linz, Institute of Inorganic Chemistry, Austria.
Electronic Supplementary Information (ESI) available: [details of any supplementary
information available should be included here]. See DOI: 10.1039/x0xx00000x
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3PS* is converted back to the ground state mainly by the energy
transfer to O2 leading to formation of O2. Thus, the population
of 3PS* can be estimated by quantification of 1O2. We observed
that both [Sn(P~OH)Cl2] and [In(P~OH)Cl] are efficient catalysts
for 1O2 generation (Figure S19) indicating that their triplet states
are populated upon their excitation with red light.
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1
DOI: 10.1039/D0CC03086D
3
Next, we investigated photocatalytic properties of
[Sn(P~OH)Cl2] in aqueous buffered solutions containing sodium
ascorbate (10 mM) as a bulk reducing agent. We selected azo
dye BHQ2-R (Scheme 1B) as an organic substrate. In control
experiments we confirmed that in aqueous solutions BHQ2-R
(10 µM) is photostable when irradiated with red light for 30 min
(Figure S20). [Sn(P~OH)Cl2] is partially (~25 %) bleached under
these conditions (Figure S21). A mixture of BHQ2-R (10 µM) and
[Sn(P~OH)Cl2] (2 µM) was found to be stable for at least 30 min
when kept in the dark. However, when the latter mixture was
irradiated with red light, BHQ2-R was fully decomposed in 15
min (plot “BHQ2-R + [Sn(P~OH)Cl2] / +h”, Figure S20). The
Scheme 1. A: A nucleic acid-templated photoreduction reaction triggered by red light;
Substrate: an oligodeoxyribonucleotide (ODN) conjugate carrying 3’-TMR (N,N,N’,N’-
tetramethylrhodamine) and 5’-S, where S is an azobenzene dye (e.g. S1 and S2 in Scheme
2); Catalyst: conjugate of ODN or peptide nucleic acid (PNA) with a photosensitizer PS
(its structure is shown in inset B). B: Reduction of azobenzene derivative BHQ2~R
catalyzed by a photosensitizer PS~OH upon irradiation with red light (h) with formation
of a colourless product P-R*; [H]: bulk reducing agent (sodium ascorbate).
complete conversion of BHQ2-R under these conditions
indicates that [Sn(P~OH)Cl2] can reach at least 5 catalytic
turnovers. We found that another azo dye BHQ1-R is also
photoreduced as efficiently as its analogue BHQ2-R (Figure S22).
Unexpectedly, [In(P~OH)Cl] is not a catalyst of BHQ1-R and
BHQ2-R photoreduction.
According to the study of PS~OH/BHQ1 interactions by
molecular dynamics simulations (Figures S23, S24), [In(P~OH)Cl]
can form a non-covalent complex with the substrate due to
are prone to aggregation and their synthesis is low yielding.23-25
In contrast, both In(III) and Sn(IV) complexes of PH2~OH are
substantially more photostable and can be obtained in
relatively high yield. [In(P~OH)Cl] has been previously studied in
hydrophobic segregation and
--stacking interactions.
However, the aromatic systems of the catalyst and the
substrate are laterally shifted leading to less efficient overlap
(Figure S23, left). In contrast, in the modelled
[Sn(P~OH)Cl2]/BHQ-1 complex both aromatic systems stack
over one another that should enable the efficient photoinduced
electron transfer from the excited state of [Sn(P~OH)Cl2] to the
substrate (Figure S23, right). Furthermore, we observed that
ascorbate inhibits [Sn(P~OH)Cl2] much more efficiently than
[In(P~OH)Cl] in the reaction of 1O2 formation (Figure S25).
Correspondingly, photoreduction pathway in the former case is
more preferable than 1O2 generation. A possible reason for that
is stronger binding of ascorbate to the more electron deficient
Sn(IV) centre.
Next, we confirmed that the activity of [Sn(P~OH)Cl2] is not
limited to photoreduction of azo dyes. This catalyst can induce
conversion of fluorescein to its leuco form and transform
aromatic azides to amines (Figure S26). However, one has to
apply a substantial excess of the catalyst (10 eq) to enable these
reactions, whereas the reduction of BHQ2-R and BHQ1-R occurs
even in the presence of only 0.2 eq catalyst.
To evaluate whether the photoreduction of azo dyes could be
conducted in the nucleic acid-templated fashion, we prepared
conjugates of the catalysts and the substrates with either
oligodeoxyribonucleotides (ODNs) or their analogues peptide
nucleic acids (PNAs). Both ODNs and PNAs are able to bind to
target nucleic acids in a sequence specific manner thereby
supporting the templated reactions (Scheme 1A). First, we
synthesized conjugate 1a containing [In(P)Cl] attached to the 3’-
terminus of ODN1 (Schemes 1, 2) as described elsewhere.23-25
1
the group of Mokhir as a photosensitizer for O2 generation.23-
29
Furthermore, Knör and co-workers have demonstrated that
Sn(chlorin)X2 (X= OH, Cl) generated in situ from the
corresponding Sn-porphyrins can act as light-harvesting
sensitizers by recycling rhodium hydride [Cp*Rh(bpy)H]+.22
We prepared [In(P~OH)Cl] as previously described.23 The
protocol for synthesis of [Sn(P~OH)Cl2] is provided in the
supporting information (SI). Analogous Sn complexes with
chlorine e630 and related ligands31 were known.
UV-visible spectra of PH2~OH, [In(P~OH)Cl] and [Sn(P~OH)Cl2]
dissolved in CH3CN are shown in Figure S17 (left plot, SI). They
all feature a strong absorbance band at ~655 nm and, therefore,
were expected to be well responsive to red light. We found that
the fluorescence from the complexes was weaker than that of
the ligand under similar conditions (Figure S17, right plot). This
indicates the higher triplet (3PS*) quantum yield in [In(P~OH)Cl]
and [Sn(P~OH)Cl2]. UV-visible spectra of the complexes are
practically not changed when CH3CN solvent is replaced with
aqueous buffered at pH 7 solution (Figure S18). However, the
dependences of intensities of absorbance bands at 415 and 655
nm from the concentration of the complexes PS~OH deviate
significantly from Beer-Lambert’s law at [PS~OH]> 2.5 µM.
These data indicate aggregation of these coordination
compounds. Therefore, when possible, all experiments
described in this paper were conducted at [PS~OH]< 2.5 µM.
Photoreductive properties of PS~OH’s rely on the formation of
their long-lived triplet state (3PS*) upon the excitation with red
light (Figure S19). In the absence of bulk reducing agents the
2 | J. Name., 2012, 00, 1-3
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This compound was used as a negative control. Attempts to (Scheme 2, 3). Synthetic details of conjugate preparation are
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DOI: 10.1039/D0CC03086D
obtain analogous conjugate containing [Sn(P)Cl2] (1b) were not provided in the SI. >90 % Purity of all conjugates was confirmed
successful due to oxidative decomposition of [Sn(P)Cl2] during by HPLC and their identity - by MALDI-TOF mass spectrometry
the synthesis. We solved this problem by replacing ODN1 for (SI).
peptide nucleic acid PNA1. Resulting conjugate
2 was Analogously to unconjugated substrates azobenzene
successfully obtained by solid phase synthesis as described in derivatives in both 3a and 3b are susceptible to the
the SI. Next, we prepared two substrates 3a and 3b, where photoreduction in the presence of [Sn(P)Cl2], but not [In(P)Cl]
azobenzene derivatives S1 and S2 were attached to the 5’- (Figure 2A). In solution substrate 3a (100 nM) exhibits low
terminus of ODN2 (Schemes 2, 3)
emission intensity of 4 + 2 a.u. (λex= 550 nm, λem= 580 nm)
indicating strong quenching of the TMR dye due to its
interaction with substrate S1 (Figure 1B, trace 1). Addition of
the catalyst
emission. In contrast, addition of complementary DNA2 (1 eq)
to solution of 3a or to the equimolar mixture of 3a and leads
2 (1 eq, trace 2) to 3a practically does not affect the
2
to the 7.7-fold fluorescence increase in both cases indicating
formation of duplexes. Irradiation of the equimolar mixture
3a/2/DNA2 with red light induces the reduction of substrate S1
in 3a that is reflected in the fluorescence increase (trace 4) that
is 12-fold faster than in the absence of the template (trace 3).
The fluorescence of control mixture 4/2/DNA2 remains stable
upon its irradiation with red light (trace 5). To evaluate whether
the distance between the substrate and the catalyst in the
templated reaction affects its rate, we introduced to DNA2 gaps
of 1, 2 and 3 “T”-residues (Figure 1C, Scheme 3). We observed
the clear drop in the reaction rate with increasing the distance
between the reactants that is an expected outcome for the
templated reaction mediated by photoinduced electron
transfer.32 Furthermore, we confirmed that the reaction is
highly sensitive to even single mismatches in the template
(Figure 1D).
In contrast to 3a, 3b was found to be inactive in the templated
reaction despite the fact that S1 and S2 exhibit comparable
reactivity in the presence of [Sn(P~OH)Cl2] (Figure 1A). This
might be an indication that the mutual orientation of the
catalyst and the substrate on the template required for the
electron transfer cannot be achieved for S2.
Scheme 2. Structures of catalysts (inset
A), substrates (inset B) as well as controls
(
inset C) used in this study. Structures of dyes TMR and FAM are shown in inset C.
Sequences of ODN1 and ODN2 as well as PNA1 are given in Scheme 3.
Finally, we tested whether the photoreduction occurs at lower
concentrations of the reagents (Figure S36, Table S1, SI). We
observed that at 20 nM of
2 and 3a the reaction is still
accelerated by 3.6 fold in the presence of 1 eq DNA2. The
decreasing of the template-induced acceleration can be
explained by limited DNA binding affinity of catalyst 2, which
contains only a 6-mer PNA sequence. This is confirmed by the
fact that the templated reaction at 5 nM of the reagents is not
significantly faster than the non-templated reaction. However,
Scheme 3. Sequences of ODN1 and ODN2 as well as PNA1 and DNA templates aligned to
indicate sequence regions, which complementary to each other.
at the conditions forcing the binding of catalyst
2 to DNA2 (2-
fold excess of ) the templated reaction is 5.2-fold faster than
2
and N,N,N’,N’-tetramethylrhodamine (TMR)
– to its 3’-
the non-templated one (Table S2). These data indicate that
further improvement of the sensitivity of the newly developed
templated photoreduction can be achieved by increasing
terminus. Substrates S1 and S2 are both azobenzene
derivatives, one of which is more electron deficient (S1) than
another (S2). TMR was used as a fluorescent probe. S1 is a
strong quencher, whose visible light absorbance band overlaps
with the emission of TMR. Therefore, we expected that the TMR
dye in intact 3a will be quenched, but recover its fluorescence
upon photoreduction of S1. The azobenzene fragment S2 is not
a quencher of TMR. Therefore, we added a fluorescein (FAM)
residue to S2 to enable the efficient quenching of TMR in intact
affinity of catalyst
2 to DNA templates. That would be possible
e.g. by using longer PNA sequences.
In summary, we developed the first red light dependent nucleic
acid templated photoreduction, which is highly sequence
specific, provides for ~12-fold template-induced rate
acceleration and allows detecting down to 20 nM nucleic acids.
Best known photochemical templated reactions triggered by
3b. As a control we used conjugate 4 lacking any 5’-modification
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J. Name., 2013, 00, 1-3 | 3
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2
K. Gorska, N. Winssinger, Angew. Chem. Int. Ed., 2013, 57,
View Article Online
visible light are similarly sequence specific, can reach over 100-
fold template-induced rate acceleration and are able to detect
down to 0.1 pM nucleic acids.33,34 We envision that after
improving sensitivity limit (e.g. by using catalysts with longer
PNA sequences) and rate acceleration (e.g. by optimization of
reducible substrates and substrate/catalyst orientation on the
template), our reaction can become a highly useful addition to
the currently available repertoire of photochemical nucleic
acid-templated reactions. It will offer a critical advantage over
the known systems of using mild and, therefore, non-toxic
trigger: red light.
6820.
DOI: 10.1039/D0CC03086D
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5
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3a / [In(P~OH)Cl]
2
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Figure 1. A: Dependence of initial rate of photoreduction of 3a and 3b upon irradiation
with red light ((dF/dt)t=0, where F is emission intensity, λex= 550 nm, λem= 580 nm) from
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Notes and references
‡
This project is funded by German Research Council (DFG, MO1418/8-1). Support
of G.K. by the Austrian Science Fund (FWF project W-1250 DK9: "Photochemical
Control of Cellular Processes") is also gratefully acknowledged. The partial support
was provided by DFG/RSF (DFG MO 1418/11-1, RSF 19-44-04111(DNA template azo
dye reduction)) and Emerging Field Initiative of Friedrich-Alexander-University of
Erlangen-Nürnberg, project “Chemistry in live cells”.
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Graphical Abstract
e-
[H]
650 nm
Dye
Substrate
Photocatalyst
Cat
Cat
Dye
S
Nucleic Acid