Frederico A Baptista1, Dorottya Krizsan1, Mark Stitch1, Igor V Sazanovich2, Ian P Clark2, Michael Towrie2, Conor Long3, Lara Martinez-Fernandez4, Roberto Improta5, Noel A P Kane-Maguire6, John M Kelly7, Susan J Quinn1. 1. School of Chemistry, University College Dublin, Dublin 4, Ireland. 2. STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, U.K. 3. The School of Chemical Sciences, Dublin City University, Dublin 9, Ireland. 4. Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry(IADCHEM) Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain. 5. Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80136 Naples, Italy. 6. Department of Chemistry, Furman University, 3300 Poinsett Highway, Greenville, South Carolina 29613-1120, United States. 7. School of Chemistry, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
Abstract
Assessment of the DNA photo-oxidation and synthetic photocatalytic activity of chromium polypyridyl complexes is dominated by consideration of their long-lived metal-centered excited states. Here we report the participation of the excited states of [Cr(TMP)2dppz]3+ (1) (TMP = 3,4,7,8-tetramethyl-1,10-phenanthroline; dppz = dipyrido[3,2-a:2',3'-c]phenazine) in DNA photoreactions. The interactions of enantiomers of 1 with natural DNA or with oligodeoxynucleotides with varying AT content (0-100%) have been studied by steady state UV/visible absorption and luminescence spectroscopic methods, and the emission of 1 is found to be quenched in all systems. The time-resolved infrared (TRIR) and visible absorption spectra (TA) of 1 following excitation in the region between 350 to 400 nm reveal the presence of relatively long-lived dppz-centered states which eventually yield the emissive metal-centered state. The dppz-localized states are fully quenched when bound by GC base pairs and partially so in the presence of an AT base-pair system to generate purine radical cations. The sensitized formation of the adenine radical cation species (A•+T) is identified by assigning the TRIR spectra with help of DFT calculations. In natural DNA and oligodeoxynucleotides containing a mixture of AT and GC of base pairs, the observed time-resolved spectra are consistent with eventual photo-oxidation occurring predominantly at guanine through hole migration between base pairs. The combined targeting of purines leads to enhanced photo-oxidation of guanine. These results show that DNA photo-oxidation by the intercalated 1, which locates the dppz in contact with the target purines, is dominated by the LC centered excited state. This work has implications for future phototherapeutics and photocatalysis.
Assessment of the DNA photo-oxidation and synthetic photocatalytic activity of chromium polypyridyl complexes is dominated by consideration of their long-lived metal-centered excited states. Here we report the participation of the excited states of [Cr(TMP)2dppz]3+ (1) (TMP = 3,4,7,8-tetramethyl-1,10-phenanthroline; dppz = dipyrido[3,2-a:2',3'-c]phenazine) in DNA photoreactions. The interactions of enantiomers of 1 with natural DNA or with oligodeoxynucleotides with varying AT content (0-100%) have been studied by steady state UV/visible absorption and luminescence spectroscopic methods, and the emission of 1 is found to be quenched in all systems. The time-resolved infrared (TRIR) and visible absorption spectra (TA) of 1 following excitation in the region between 350 to 400 nm reveal the presence of relatively long-lived dppz-centered states which eventually yield the emissive metal-centered state. The dppz-localized states are fully quenched when bound by GC base pairs and partially so in the presence of an AT base-pair system to generate purine radical cations. The sensitized formation of the adenine radical cation species (A•+T) is identified by assigning the TRIR spectra with help of DFT calculations. In natural DNA and oligodeoxynucleotides containing a mixture of AT and GC of base pairs, the observed time-resolved spectra are consistent with eventual photo-oxidation occurring predominantly at guanine through hole migration between base pairs. The combined targeting of purines leads to enhanced photo-oxidation of guanine. These results show that DNA photo-oxidation by the intercalated 1, which locates the dppz in contact with the target purines, is dominated by the LC centered excited state. This work has implications for future phototherapeutics and photocatalysis.
The role of transition
metal complexes in causing photo-oxidation
in DNA is well established, and they are increasingly being considered
as an alternative to porphyrins for light-activated therapeutic applications.[1−6] Many (perhaps most) of these complexes are expected to generate
singlet oxygen which can then attack cellular biomolecules, including
nucleic acids.[1−6] However, another possible mechanism, which has become apparent over
the past few years, is the direct oxidation of guanine and DNA damage
by photoinduced one-electron abstraction by the excited state of a
proximal metal complex.[7−11] In order to facilitate such a reaction with DNA one can incorporate
ligands that will cause the complex to bind strongly to DNA with well-defined
geometry. This can be achieved using complexes containing a ligand
which can intercalate between the base pairs of DNA. One class of
such metal complexes, which has been much studied over recent years,
is that containing (dipyrido[3,2-a:2′,3′-c]phenazine), (dppz) such as [Ru(phen)2(dppz)]2+ (phen = 1,10 phenanthroline).[12] An additional feature of these complexes is that they exist
as enantiomers,[13,14] which can show different DNA-binding
and photophysical properties. [Ru(phen)2(dppz)]2+ is itself unable to photo-oxidize DNA, but it is possible to increase
the oxidizing power of the excited state by changing the ligand (for
example replacing phen by 1,4,5,8-tetraazaphenanthrene (TAP)[8]) or by replacing the metal (e.g., with chromium).Exploration of the photochemistry and photophysics of Cr(III) systems
is second only to ruthenium(II) among the transition metals.[15−22] Recently the potential to tune their photophysical properties to
enhance their photonic and photocatalytic behavior has attracted considerable
attention.[23−29] Upon photoexcitation chromium complexes are known to be more strongly
oxidizing than their ruthenium counterparts, and in the case of Cr(diimine)33+ complexes the oxidizing power of the relatively
long-lived (μs) lowest doublet metal-centered 2E/2T1 (2MC) excited state is of the order
of 1.4 V v SHE.[18−20] Furthermore, in contrast to the Ru(diimine)32+ complexes, whose excited state chemistry is dominated
by metal-to-ligand-charge-transfer (MLCT) processes, other excited
states, including ligand-centered (LC) states, are available to chromium
systems. In addition, such LC states are expected to be of significantly
higher energy than the long-lived LC ππ* triplet state
observed for ruthenium complexes containing the extended dppn (benzo[i]dipyrido[3,2-a:2′,3′-c]phenazine) ligand, which damages DNA through sensitized
singlet oxygen formation.[30,31]It has been shown
by our groups that [Cr(phen)2(dppz)]3+ and related
complexes bind strongly to double-stranded DNA
and that this is accompanied by the quenching of the emission of the
Cr-complex, which is consistent with its excited state being capable
of oxidizing guanine.[32−37] It was also found that the luminescence of [Cr(phen)2(dppz)]3+ is dynamically quenched by 5′-guanosine
monophosphate (GMP) with a rate constant close to that of diffusion
control, while 5′-adenosine monophosphate (AMP) was almost
3 orders of magnitude less effective.[34] Though the behavior with GMP is entirely consistent with quenching
via electron transfer, no evidence of the reduced complex could be
found using nanosecond flash photolysis,[33,34] suggesting that the back reaction with the oxidized GMP must also
be very fast.Time-resolved infrared spectroscopic (TRIR) measurements
have been
shown to be particularly valuable for studying transient species from
intercalator-DNA systems, as the spectra can provide information not
only about the intercalator but also about the behavior of the host
DNA site, which is revealed by “bleach” bands in the
1600–1750 cm–1 region.[10,38−42] TRIR also allows detection of the guanine radical cation, which
absorbs at 1700 cm–1.[7,43,44] Such data are not readily obtainable by visible transient
absorption (TA), as generally DNA transient species only absorb weakly
at wavelengths >400 nm.[40] We have extensively
studied the photo-oxidizing complex [Ru(TAP)2dppz]2+ (E0(*Ru2+/Ru+), = 1.44 V vs SHE) using picosecond TA and TRIR[40] and have correlated the photophysical properties
in solution to structural data obtained by X-ray studies on the DNA
bound systems.[40,45,46] More recently we investigated the electron transfer reaction of
racemic rac-[Cr(phen)2(dppz)]3+ bound to guanine-containing oligodeoxynucleotides (ODNs) using
these techniques and discovered that in those cases the excited state
was quenched with rates faster than 3 ps.[35]The unsubstituted TAP and phen allow deep intercalation of
the
dppz ligand, and X-ray crystallography reveals that the isostructural
complexes bind in a similar fashion.[40] However,
the presence of bulky ancillary ligands has been found to influence
the DNA binding site. In particular, dppz complexes with 3,4,7,8 tetramethyl-1,10-phenanthroline
(TMP) as an ancillary ligand have been found to show a preference
for AT DNA.[32,36,47,48] This was reported for the Cr(TMP)2dppz3+ (1)[32] and
related complexes[36] and subsequently for
the Ru(TMP)2dppz system.[47] In
the case of the ruthenium system theoretical studies showed preference
for binding from the minor groove to d(ATATAT)2 over d(GCGCGC)2.[48] Interestingly, Barton and co-workers
showed that the presence of the bulky ancillary ligands demonstrated
a preference for mis-match DNA.[49]In the ultrafast spectroscopic study below we examine the photo-oxidation
of DNA by each of the enantiomers of [Cr(TMP)2dppz]3+ and particularly of the lambda enantiomer which the Kane-Maguire/Wheeler
group has previously reported demonstrates a strong preferential binding
to DNA and most prominently for AT-rich polynucleotides.[32] This complex therefore has the potential to
target AT-rich sites, such as the TATA box.[50] Here, we report the steady state and ps-/ns-transient spectroscopic
studies of the lambda and delta enantiomers of [Cr(TMP)2(dppz)]3+ bound to four ODN systems, namely the self-complementary
sequences d(GCGCGCGCGC)2, d(CGCGAATTCGCG)2, d(CGCAAATTTGCG)2, and d(ATTATTATTATATTA)/d(TAATATAATAATAAT)
duplex (AT DNA), as well as to natural (salmon testes, ST-DNA) DNA, Figure . Together the AT
base-pair content of these systems range from 0% to 100%. Significantly
these studies reveal a role for upper (dppz-localized) excited states
in the oxidation of the adenine (as well as the guanine) nucleobases
forming the radical cations, which are identified by TRIR. To the
best of our knowledge this is the first case where the LC state of
a Cr(diimine)33+ complex participates in direct
electron transfer with purine bases and the first observation of an
intercalating metal complex sensitizing adenosine oxidation in DNA.
Figure 1
Structure
of [Cr(TMP)2dppz]3+ complex (1)
together with double stranded DNA systems aself-complementary
and bwith the complementary strand 5′-TAATAATAATATAAT-3′.
Structure
of [Cr(TMP)2dppz]3+ complex (1)
together with double stranded DNA systems aself-complementary
and bwith the complementary strand 5′-TAATAATAATATAAT-3′.
Results
Steady State Spectroscopic
Study of DNA Binding
rac-[Cr(TMP)2(dppz)]Cl3 (1) was prepared as previously
reported,[51] and its enantiomers were resolved
by passing the racemic compound
through a C25-sephadex column eluted with a (−)-O,O′-dibenzoyl-l-tartrate mobile
phase. The UV–visible and circular dichroism (CD) spectra of
the resolved samples (Λ-; 76.5% and
Δ-1; 79.0%) are shown in Figure S1 and indicate details summarized in Table S1. The near-UV region of the spectrum (300–380 nm)
is dominated by a structured band, showing peaks at 360 and 377 nm,
which may be assigned to a dppz ligand-centered (LC) (ππ*)
transition.[32] In the visible region weak
peaks at approximately 425 and 457 nm are ascribed to the metal-centered
(d–d) (4A2 → 4T2 (Oh) transitions. Excitation of the complex in
the near UV or visible region results in a sharp emission at 737 nm,
assigned to the 2E/2T1 → 4A2 transition from a doublet metal-centered (2MC) state (Figure S2).The
emission of 1 is found to be quenched in the presence
of GMP. Notably, 5′-deoxyadenosine monophosphate (dAMP) is
also observed to quench the emission but significantly less effectively.
Stern–Volmer plots show that quenching occurs for GMP with
a kq value of 1.7 × 109 dm3 mol–1 s–1, close
to the diffusion limit, while a lower rate constant of 4.2 ×
106 dm3 mol–1 s–1 is observed for dAMP (see Figure S3).
This result is similar to that observed for the Cr(phen)2dppz complex.[34] Titrations of the enantiomers
with aliquots of the various DNA/ODN samples shown in Figure were performed and monitored
by UV/visible and emission spectroscopy (Figures and S4–S5). In all cases a diminution of the absorbance of the peaks at 360
and 377 nm (associated with the ππ* transitions of the
dppz ligand) was observed, with a well-defined isosbestic point at
388 nm and enhanced absorption at wavelengths beyond that (Figure S4). Such behavior is consistent with
intercalation of the dppz ligand.[32,33]
Figure 2
(a) UV–vis
spectra and (b) emission of 10 μM Λ-1 increasing
concentrations of CGCAAATTTGCG (0–230
μM Nucleobase) in the presence of 50 mM potassium phosphate
buffer, pH 7. Normalized intensity at 737 nm for (c) Λ-1 and (d) Δ-1 in the presence of the different
DNA sequences (Excitation at 373 nm).
(a) UV–vis
spectra and (b) emission of 10 μM Λ-1 increasing
concentrations of CGCAAATTTGCG (0–230
μM Nucleobase) in the presence of 50 mM potassium phosphate
buffer, pH 7. Normalized intensity at 737 nm for (c) Λ-1 and (d) Δ-1 in the presence of the different
DNA sequences (Excitation at 373 nm).Monitoring the emission demonstrates that in each case the emission
at 737 nm is at least partially quenched upon addition of aliquots
of the DNA or ODN (Figure c–d and Figure S5). In contrast
to the dynamic quenching observed in the presence of GMP and dAMP,
it is expected that for the DNA or ODN systems the process will involve
static quenching as was previously shown for the analogous [Cr(phen)2dppz3+].[34] Plots of
the absorbance (Figure a, Figure S4) and emission (Figure b, Figure S5) changes reveal that in all cases the effect is larger for
the lambda complex than for its delta enantiomer consistent with it
binding more strongly. Binding constants derived from the emission
data using the Bard equation[52] are given
in Table S2, and the fitted data are shown
in Figure S6. The comparison of the emission
titrations (Figure c–d) indicates that the emission quenching at [Nucleobase]/[Cr]>20
is high in all cases (>90%) for guanine-containing DNAs. Importantly,
significant quenching (ca. 60%) is observed for the d(ATTATTATTATATTA)/(TAATATAATAATAAT)
sequence, indicating that the excited state can be deactivated by
adenine. Differences in the binding behavior of the Λ and Δ
enantiomer are most apparent for the CGCGAATTCGCG, CGCAAATTTGCG,
and ST-DNA DNA systems with the largest effect found for CGCAAATTTCGC
(see Figure S4).
ps- and ns-Transient Absorption
(TA) of [Cr(TMP)2(dppz)]3+ in Solution
To understand the mechanisms
for quenching of the excited state of [Cr(TMP)2(dppz)]3+ by the various DNA systems, we first investigated the behavior
of [Cr(TMP)2(dppz)]3+ in D2O or D2O/buffer solutions. Figure (and Figure S7) shows the
results of TA experiments, monitoring on both picosecond and nanosecond
time scales following excitation at 355 or 373 nm. Similar results
were obtained in both D2O and D2O/50 mM potassium
phosphate buffer. It may be observed that 1 ps after excitation a
new species is present which shows maximum absorption at 469 nm and
several prominent shoulders. This transient spectrum is similar to
that previously observed for dppz itself[53] and for [Re(CO)3py(dppz)]+[54] and assigned to a ππ* excited state. It is
therefore consistent with this initially formed species from 1 being a ligand-centered (LC) excited state. The absorbance
at 469 nm then partially decays which can be modeled by biexponential
kinetics with lifetimes of 4.3 ps (28%) and 460 ps (23%) with the
remainder decaying at longer times. We propose that the first species
observed is the LC-state [4Cr(TMP)21dppz]3+* and that this species then decays with a lifetime
of 4.3 ps via intersystem crossing to [4Cr(TMP)23dppz]3+*. TD-DFT simulations (see Supporting Information (SI) for details), which
we have shown to be reliable for similar metal complexes,[41,55] were carried out for this latter species and show indeed that it
is predicted to have a strong transient absorption band in this spectral
region (Figure S8).
Figure 3
ps-ns-TA spectrum of
1 mM of -1 in the presence
of 50 mM of sodium phosphate buffer in
D2O (excitation 373 nm (ps)/355 nm (ns)).
ps-ns-TA spectrum of
1 mM of -1 in the presence
of 50 mM of sodium phosphate buffer in
D2O (excitation 373 nm (ps)/355 nm (ns)).Probing 1 on the nanosecond time scale (up to
500
ns) reveals a major change as the species showing maximum absorption
at 469 nm decays with a lifetime of 4 ns and a new species possessing
a broad absorption band with a maximum at ca. 530 nm is formed (see Figure ). This latter species
decays away only very slowly indicating that it has a lifetime greater
than 500 ns, as expected for an emissive 2MC excited state.[34,35] It is clear from these ps and ns TA experiments that excitation
in the range 350–400 nm produces LC-species with rather long
lifetimes, and it is intriguing to consider whether they might react
when bound to DNA, which could be most readily observed by TRIR.
Time-Resolved Infrared (TRIR) Studies of [Cr(TMP)2(dppz)]3+ in Solution
ps- and ns-TRIR experiments
were first carried out on the [Cr(TMP)2(dppz)]3+ solutions under comparable conditions to those used for the TA (see SI). Ground state IR (FTIR) spectrum of 1 recorded in D2O is highly structured arising
from vibrations on the TMP and dppz ligands (Figure ). This solution spectrum is found to be
in excellent agreement with the spectrum simulated using unrestricted
DFT calculations (see Experimental Section). These simulations were used to assign vibrations of the complex
(Table S3, Figure S9), including those
localized on the two TMP ligands (observed to occur at 1635 cm–1 (CH3 phen coupled) and 1540 cm–1 (C=N phen)) and dppz based vibrations at 1495 and 1505 cm–1.
Figure 4
(a) Comparison of the calculated (B3LYP/LanL2DZ; see SI for further details) and experimental infrared
spectra of 1. *Absence of the band at 1460 cm–1 in the ground state FTIR arises due to imperfect blank against D2O solution containing contributions from HOD. (b) Highlighted
key simulated dppz and TMP ground state vibrations.
(a) Comparison of the calculated (B3LYP/LanL2DZ; see SI for further details) and experimental infrared
spectra of 1. *Absence of the band at 1460 cm–1 in the ground state FTIR arises due to imperfect blank against D2O solution containing contributions from HOD. (b) Highlighted
key simulated dppz and TMP ground state vibrations.TRIR spectra commonly show characteristic positive absorption
bands
of the transient species and also negative “bleach”
bands due to depletion of the ground state. Spectra at selected times
following 150 fs 400 nm excitation of [Cr(TMP)2(dppz)]3+ in D2O phosphate buffer solution are shown in Figure . Between 1 and 10
ps (where a significant diminution of the TA band at 469 nm was observed)
a strong growth of a sharp band at 1512 cm–1 is
seen. Subsequently, over the next nanosecond this band partially diminishes,
and simultaneously, transient bands at 1502 and 1531 cm–1 are strengthened and the bleach at 1539 cm–1 associated
with TMP vibrations increases. By 100 ns, when we anticipate that
the 2MC is formed, one can see that the bleach pattern
is in good agreement with that of the FTIR absorption bands (Figure a). Each of these
bands are accompanied at lower wavenumber by absorption bands which
we assign to the 2MC state. The spectra at shorter times,
especially in the 1500–1550 cm–1 region,
provide further insights into the complex interconversion of species
eventually leading to this low-lying state. In the spectrum at 1 ps
it may be noted that the bleaching of the vibration at 1505 cm–1 (dppz) is much stronger than that at 1539 cm–1 (TMP) in contrast to what is found in the FTIR. This
indicates that the frequency of this TMP-localized vibration is essentially
unaffected upon formation of the excited state, as expected for a
purely dppz-localized excited state. The subsequent increase in the
bleaching intensity of this band is consistent with the formation
of the MC state and the consequent changes in the bonding to the TMP.
Kinetic analysis of the grow-in of the transient at 1530 cm–1 and the bleach 1539 cm–1 reveals a process on
the 5 ns time scale (Figure S10), which
is in good agreement with the TA (Figure ). As noted above from the TA measurements
we propose that initial excitation leads to the formation of the singlet
dppz-centered excited state [4Cr(TMP)2(1dppz)]3+, which leads to the formation of a [4Cr(TMP)2(3dppz)]3+ (5 ps)
(eq ). DFT calculations
predict that this latter species shows the characteristic sharp band
10 cm–1 higher than the ground state vibration found
experimentally at 1505 cm–1 (Figures b, S11, and S12) A further currently unassigned species is then formed which then
yields the long-lived 2MC state (eq ).
Figure 5
(a) ps-ns-TRIR spectrum of 1 mM of -[Cr(TMP)dppz] in the presence of 50 mM of sodium phosphate
buffer in D2O upon 400 nm (5 kHz, 1 μJ) excitation.
(b) Calculated (see SI for details) dppz
LC vibrations of the [4Cr(TMP)2(3dppz)]3+ excited state species.
(a) ps-ns-TRIR spectrum of 1 mM of -[Cr(TMP)dppz] in the presence of 50 mM of sodium phosphate
buffer in D2O upon 400 nm (5 kHz, 1 μJ) excitation.
(b) Calculated (see SI for details) dppz
LC vibrations of the [4Cr(TMP)2(3dppz)]3+ excited state species.
Time-Resolved DNA Studies
ps-Time-Resolved Infrared (TRIR) of 1 in a GC ODN
To investigate the photochemical and
photophysical processes occurring
when 1 is excited when bound to DNA, the TRIR spectra
of a series of defined-sequence ODNs (Figure ) were next recorded. In general, the results
involving the lambda and delta enantiomers are similar, and we will
focus initially on the lambda species.First, we consider the
case when the lambda enantiomer is bound to an ODN possessing only
G and C nucleobases - d(GCGCGCGCGC)2. As noted above, the
emission of 1 is strongly quenched in the presence of
d(GCGCGCGCGC)2 at high [Nucleobase]/Cr ratios (Figure c). TRIR spectra
(at [Nucleobase]/Cr = 20, where the quenching is >95%) recorded
from
1 ps to 2.8 ns after laser excitation (50 fs; 373 nm) are shown in Figure a. These spectra
show bleach bands characteristic of the metal complex, which are dwarfed
by those corresponding to the carbonyl vibrations of the C (1650 cm–1) and G (1680 cm–1) nucleobases.
The bleaching of the nucleobase bands is similar to that found for
the oxidation of guanine in base-paired ODNs, as reported with other
DNA-intercalated dppz complexes.[40,41] There is also
a weak absorption band at ca. 1700 cm–1, where it is predicted from DFT studies that the guanine radical
cation (G•+) absorbs.[43,56−58] It may also be noted that the pattern of the bleaches for the metal
complex is quite different from that found for 1 in solution.
This suggests that the excited state initially formed by the excitation
pulse ([4Cr(TMP)2(1dppz)]3+) reacts with the ODN on a subpicosecond time scale, i.e. faster
than the formation of the triplet state [4Cr(TMP)2(3dppz)]3+. We propose that the species observed
on the picosecond time scale is [4Cr(TMP)2(dppz)]/(GC) contact ion pair. In contrast to 1 in solution, its characteristic transient and bleach bands are found
to decay and recover rapidly without evolution of the spectral structure.
The bleach bands of the Cr-complex recover at the same rate as those
of the nucleobase which follow biphasic kinetics lifetimes of 3.7
ps (63%) and 42 ps (37%) (see Figure b–c). It may be noted that at 1 ns the signal
at 1505 cm–1and 1540 cm–1 is very
weak indicating the almost total suppression of the 2MC
state, or other excited states/transient species. We ascribe this
to back electron transfer reforming the ground state (eq ).
Figure 6
(a) ps-ns-TRIR
spectrum of 1 mM of Λ-1 in the
presence of 25 mM nucleotide of d(GCGCGCGCGC)2 in 50 mM
of sodium phosphate buffer in D2O (λexc = 373 nm, 5 kHz, 1 μJ). Kinetics showing recovery of (b) the
metal complex bleach at 1538 cm–1 and (c) guanine
carbonyl at 1683 cm–1.
(a) ps-ns-TRIR
spectrum of 1 mM of Λ-1 in the
presence of 25 mM nucleotide of d(GCGCGCGCGC)2 in 50 mM
of sodium phosphate buffer in D2O (λexc = 373 nm, 5 kHz, 1 μJ). Kinetics showing recovery of (b) the
metal complex bleach at 1538 cm–1 and (c) guanine
carbonyl at 1683 cm–1.
ps-Time-Resolved Infrared (TRIR) of 1 in an AT ODN
Considering
the TRIR of 1 bound to the d(ATTATTATTATATTA)/d(TAATATAATAATAAT)
(Figure ), one can
see that as with the complex bound to d(GCGCGCGCGC)2 the
spectrum is dominated by the bleach bands for the ODN (in this case,
at 1640 cm–1 (T), 1622 cm–1 (A),
1662 cm–1 (T), 1690 cm–1 (T))
and of the complex (at 1505 and 1539 cm–1).[59,60] However, in contrast to what is found with d(GCGCGCGCGC)2 there is also a transient species showing a very strong absorption
at 1708 cm–1. This decays away rapidly (by first-order
kinetics τ = 27 ± 2 ps) and is accompanied by partial recovery
of the nucleobase bleaches (τ = 26 ± 2 ps (54%) at 1690
cm–1). The recovery of the bleaches continues within
the nanosecond time domain (1.5 ± 0.2 ns (33%)) and the residual
portion at longer times (100 ns).
Figure 7
ps-ns-TRIR (400 nm excitation) spectrum
of 1 mM of Λ-[Cr(TMP)2dppz]3+ in the presence
of 25 mM nucleobase of
(a) d(ATTATTATTATATTA)/d(TAATATAATAATAAT) duplex in 50
mM of sodium phosphate buffer in D2O. Kinetics showing
recovery of (b) the transient at 1708 cm–1 and (d)
bleach at 1690 cm–1.
ps-ns-TRIR (400 nm excitation) spectrum
of 1 mM of Λ-[Cr(TMP)2dppz]3+ in the presence
of 25 mM nucleobase of
(a) d(ATTATTATTATATTA)/d(TAATATAATAATAAT) duplex in 50
mM of sodium phosphate buffer in D2O. Kinetics showing
recovery of (b) the transient at 1708 cm–1 and (d)
bleach at 1690 cm–1.Examining the bleaches due to the complex at 1505 and 1539 cm–1, it may be noted that unlike what was observed with
d(GC)5 these bleaches only recover slightly in the picosecond
range, indicating that most of the ground state is still not reformed
by 1 ns. However, the ratio of the absorbance of the bleach bands
(A1505/A1539) changes significantly during the period, increasing up to 100 ps
and then gradually decreasing up to 3 ns. At short times (<10 ps)
broad transient absorption is also seen at 1565 and 1525 cm–1. After these bands have decayed a sharp absorption band at 1515
cm–1 is present. This feature is similar to that
observed in the TRIR of the complex itself in solution and assigned
to [4Cr(TMP)2(3dppz)]3+. At much longer times (e.g., 10 ns) the spectrum shows features,
which are similar to those of the 2MC state formed in solution
(Figure ). At this
stage the bleach bands in the nucleobase region are very weak, consistent
with the 2MC state causing very little perturbation of
these DNA-localized bands.The appearance of a reversible transient
band at 1708 cm–1 is consistent with the formation
of a short-lived DNA photoproduct,
and in the absence of guanine, we assign this to the formation of
A•+T species, as adenine is the next most readily
oxidized nucleobase.[61,62]
Characterizing the Spectral
Signatures of A•+T
In order to confirm
our hypothesis for the formation of
the A•+T species, simulated IR spectra for portions
of the AT-ODN (namely TpdApT (TAT), TpdAdA (TAA), dApTpT (ATT)) containing
the adenine cation (Ade•+) in a (dApT) dinucleotide
fragment (hereafter AT), were computed. In each case the simulated
IR spectra of Watson–Crick (WC) base-paired duplexes formed
by these species in the neutral and in the cationic form were produced
(see Figure ). These
calculations were performed at the PCM/M052X/631G(d) level (SI and methods for further details). In addition,
the inclusion of explicit D2O molecules and Na+ counterions were also considered. The number of Na+ ions
was selected in order to balance the negative charges of the phosphate
backbone, considering that a detailed characterization of the ions
location around DNA would require an extensive sampling by Molecular
Dynamics simulations and it is well beyond the scope of this study.
For what concerns D2O molecules, we selected those we expect
to be more tightly bound to the bases, i.e. the two molecules forming
hydrogen bonding (HB) with atoms not directly involved in the WC pairs
(C=O2 of Thymine, Scheme S1). The
calculated IR spectra of the neutral DNA bands in the 1600–1700
cm–1 region are in close agreement with the previously
assigned experimental values (Table S4).[59,60] These calculations reveal that the presence of Ade•+ leads to a noticeable perturbation of the local DNA structure, especially
of the WC pairing. The HB interaction with the C4=O4 WC-paired
thymine group becomes stronger, due to the larger HB accepting power
of the electron deficient Ade•+ cation. Consequently,
the thymine C4=O4 bond length increases and the associated
stretching frequencies red-shifts. This also results in a weakening
of the adenine “coupling” to the C2=O2 thymine
bond accompanied by a slight decrease in the bond, causing the stretching
frequencies to blue-shift and becoming more intense. Overall, the
C=O stretching mode is more localized on a single C=O
group. Simultaneously, the ring-stretching mode of Ade•+ red-shifts with respect to the Ade and the role of the N–H2 scissoring modes increases, since this bond acquires a partial
double bond character (the delocalization of the amino lone pair in
the electron deficient ring is favored).
Figure 8
(a) A:T Watson Crick
base pair. (b) Schematic description of the
computational AT·2 D2O system. (c) Computed difference
spectra between the cationic and the neutral forms of AT·2 D2O system. PCM/M052X/6-31G(d) calculations. Each transition
has been broadened with a Gaussian with h.w.h.m. = 10 cm–1. Harmonic spectra have been uniformly scaled by 0.955.
(a) A:T Watson Crick
base pair. (b) Schematic description of the
computational AT·2 D2O system. (c) Computed difference
spectra between the cationic and the neutral forms of AT·2 D2O system. PCM/M052X/6-31G(d) calculations. Each transition
has been broadened with a Gaussian with h.w.h.m. = 10 cm–1. Harmonic spectra have been uniformly scaled by 0.955.The computed difference (TRIR) spectrum obtained for the
AT·2D2O system is in good agreement with the experimental
one, with
the appearance of bleaches associated with both the adenine and thymine
bases and a transient band at ca. > 1700 cm–1 (see Figure c and Figure S13). There are bleaches at 1620 cm–1 (adenine), 1654 cm–1 (thymine carbonyl),
1684 cm–1 and notably the transient band at 1708
cm–1, which is in excellent agreement with the experimental
observation in Figure . The explicit D2O molecules simply red-shift (from ∼1720
cm–1 to ∼1700 cm–1) the
peaks associated with the thymine C=O groups not involved in
the interstrand HB interactions, supporting the reliability of the
predictions obtained by including solvent effect exclusively at the
PCM level. Importantly, it is confirmed that the presence of the band
at 1708 cm–1 is due to the influence of the adenine
cation on the WC paired thymine base. As detailed in Figures S13–S16, the difference spectra computed for
the different trinucleotide examined are similar to those depicted
in Figure and a similar
spectrum is obtained on the simple Ade-Thy WC dimer, confirming our
assignment of the spectra. Analogously, the computed spectra exhibit
a very small dependence on the inclusion of Na+ counterions
(compare Figures and S13), especially in the AT dinucleotide model,
suggesting that the computed difference spectra are dominated by more
“local” interactions (see also our results on the simple
WC dimer reported below) and the effect of more distant species is
more limited, especially because it could be “washed out”
by thermal fluctuations of the duplex (not considered in our treatment).Moreover, our predictions are solid not only with respect to the
detail of the model adopted (inclusion of Na+ counterions,
of explicit solvent molecules etc.) but also on the functional and
the basis set used. Interestingly, in some cases there is a dependence
on the location of the Ade•+ cation within the sequence.
The spectra obtained for the external/Solvent exposed position was
found to be in closest agreement (Figure S14) with the experimental one, which may reflect the slight opening
of the base in the presence of the complex. Notably, our calculations
predict a preference for locating the hole on the 5-′end. The
effect of the nature of the stacked base (adenine vs thymine) is rather
small, below the expected accuracy of our method. No significant delocalization
effects of the hole on two stacked bases are found[63] and the hole has a clear-cut preference for adenine bases,
indicating that the oxidation of T is not a relevant process. Finally,
as described in the SI, the computed difference
spectra for a simple AT dimer in a WC hydrogen bonded arrangement
are similar to those we have just discussed (see Figure S15), further supporting our assignment.Considering
the computational results, we therefore propose that
the TRIR spectra can be explained by the processes described by eqs –7 below. In this sequence the intercalating dppz LC excited
state is expected to oxidize adenine forming the dppz/(AT) contact radical ion pair (eq ). The formation of [4Cr(TMP)2(3dppz)]3+ could
occur either as a consequence of the back electron transfer (eq ) or by intersystem crossing
from the [4Cr(TMP)2(1dppz)]3+/(AT) (eq ). This
would be expected to be sensitive to the DNA binding site. At longer
times (e.g., at 10 ns) the TRIR spectra show that the 2MC state has been formed.
ps-Time-Resolved Infrared (TRIR) in Mixed
Sequence DNAs Sequences
Given the very different behavior
observed for 1 in
the presence of GC and AT DNA we next considered the behavior of 1 in the presence of the mixed sequence ODNs d(CGCGAATTCGCG)2 and d(CGCAAATTTGCG)2, which contain both
GC- and AT-rich regions. These can then be compared to natural (ST-DNA)
DNA which has 42% GC/58% AT. The TRIR data are presented in Figure and Figure S17.
Figure 9
ps-ns-TRIR spectra (373 nm, 5 kHz, 1 μJ)
of 1 mM of Λ-[Cr(TMP)2dppz]3+ in the presence
of 25 mM nucleotide of
(a) d(CGCGAATTCGCG)2, (b) d(CGCAAATTTGCG)2,
and (c) ST-DNA DNA in 50 mM of sodium phosphate buffer in D2O.
ps-ns-TRIR spectra (373 nm, 5 kHz, 1 μJ)
of 1 mM of Λ-[Cr(TMP)2dppz]3+ in the presence
of 25 mM nucleotide of
(a) d(CGCGAATTCGCG)2, (b) d(CGCAAATTTGCG)2,
and (c) ST-DNA DNA in 50 mM of sodium phosphate buffer in D2O.The spectrum recorded after 2
ps for Λ-1 bound
to d(CGCGAATTCGCG)2 is comparable to that recorded for
d(GCGCGCGCGC)2 with strong nucleobase bleaches at 1649
and 1678 cm–1, slightly shifted compared to the
homo-GC system (see Figure ). Bleach bands of the complex are also seen at 1505 and 1538
cm–1. These observations suggest that photoexcitation
predominantly affects G-C base pairs with less impact on the AT base
pairs. In contrast to d(GC)5, a strong transient band at
1706 cm–1 is observed. This could be attributable
to either the G•+C or A•+T species;
however, no strong AT bleaching is observed, so we assign this to
the guanine species. With Λ-1 bound to d(CGCAAATTTGCG)2 the bleach pattern of the nucleobases is again dominated
by those of G and C. However, there is an additional bleach contribution
at 1690 cm–1, indicating an increase in the perturbation
of AT base pairs. The absorption band 1705 cm–1 is
even better defined than that observed for d(CGCGAATTCGCG)2. For ST-DNA the spectrum shows a clear absorption at high wavenumbers
and some evidence of thymine bleaching, somewhat greater than found
for d(CGCGAATTCGCG)2 but much less than for the complex
bound to d(CGCAAATTTGCG)2 (see Figure ).Remarkably the spectra for these
mixed sequence systems do not
evolve substantially while they decay (see Figure a). Some residual bleaching of the nucleobase
signals (1600 and 1700 cm–1) observed after the
decay of the cation transient at >1700 cm–1 is
attributed
to perturbation by the presence of the excited state. They all show
similar kinetics, which for the nucleobase recovery can be analyzed
as a biexponential (Figure b–c). For d(CGCGAATTCGCG)2 and d(CGCAAATTTGCG)2 rapid nucleobase recovery with similar biphasic kinetics
to those observed for the bleach bands of the complex so that the
signals have substantially disappeared within 1 ns (Table , Figures S17–S18). Faster recovery of the cation transient at
1706 cm–1 is observed for these systems. These values
are close to those found for the bleach recovery observed for d(GCGCGCGCGC)2, although in that case the process was attributed to back
electron transfer of contact ion pair formed from the reduced metal
complex and the guanine radical cation.
Figure 10
Comparative TRIR spectra
of 1 mM of Λ-[Cr(TMP)2dppz]3+ in the presence
of DNA systems at 1 ps (d(ATTATTATTATATTA)/d(TAATATAATAATAAT)
at 2 ps) in 50 mM of sodium phosphate buffer in D2O. Kinetics
showing recovery of (b) the guanine carbonyl bleach and (c) photo-oxidation
transient.
Table 1
Kinetic Analysis
of DNA Systems
Λ-1
Δ-1
system
carbonyl
bleacha (ps)
transient ca. 1700a
carbonyl
bleacha (ps)
transient ca. 1700a
d(GCGCGCGCGC)2
3.7 ± 0.1 (63%); 42 ± 2 (37%)
6.0 ± 1.0b
5.2 ± 0.3 (80%); 52 ± 10(20%)
7.2 ± 2
d(CGCGAATTCGCG)2
4 ± 1 (65%); 40 ± 4 (35%)
4.4 ± 0.6 psb
6.8 ± 1.0 (74%); 55 ± 10(26%)
7.0 ± 0.8
d(CGCAAATTTGCG)2
4 ± 1 (63%); 49 ± 4 (37%)
2.0 ± 0.5 (63%); 28 ± 4 (37%)
3.9 ± 1.0 (43%); 49 ± 12(57%)
3.6 ± 1.5(43%); 39 ± 4(57%)
ST-DNA
5 ± 0.5 (61%); 72 ± 7 (39%)
10 ± 1b
8.6 ± 0.8 (67%); 101 ± 15 (33%)
2.0 ± 1.0 (60%); 31 ± 5 (40%)
Baseline referencing applied (1737
cm–1).
Best fit to a monoexponential.
Comparative TRIR spectra
of 1 mM of Λ-[Cr(TMP)2dppz]3+ in the presence
of DNA systems at 1 ps (d(ATTATTATTATATTA)/d(TAATATAATAATAAT)
at 2 ps) in 50 mM of sodium phosphate buffer in D2O. Kinetics
showing recovery of (b) the guanine carbonyl bleach and (c) photo-oxidation
transient.Baseline referencing applied (1737
cm–1).Best fit to a monoexponential.
Delta Enantiomers and DNA Systems
The major features
in the transient spectra of the delta enantiomer Δ-1 bound to the various ODN systems are broadly similar to those found
with its lambda counterpart (Figure S17). With d(GCGCGCGCGC)2 the absorption band at 1703 cm–1 is better defined and the valley between the G and
C carbonyl stretches is shallower (Figure S19). This latter feature is accentuated for d(CGCGAATTCGCG)2, where the C band almost becomes a shoulder on that of the G. For
d(CGCAAATTTGCG)2 the spectrum shows features associated
with T, as was found with the lambda enantiomer. With natural DNA
the bleach profile for the delta enantiomer more closely resembles
d(CGCAAATTTGCG)2. In general, the kinetics are longer lived
in the case of the delta enantiomer (Figure S20) which likely reflects the differences in binding.
Discussion
These experiments reveal that unlike photo-oxidizing dppz complexes
of rhenium[7,9] and ruthenium,[10] [Cr(TMP)2dppz]3+ (1) is able
to oxidize adenine. The effect is demonstrated by the partial quenching
observed in the titration observed with the ODN containing only AT
base pairs (Figure ). The origin of this quenching is due to access to relatively long-lived
dppz-localized upper excited states upon irradiation at 373 or 400
nm, as revealed by TA and TRIR experiments. The reduced quenching
observed for the AT system is attributed to the fact that the electron
transfer from the dppz LC excited state is only partially competitive
with the nonradiative processes leading to the emissive MC state.
The time-resolved experiments indicate the formation of at least two
dppz-localized excited states which lead finally to the 2MC state. Significantly, these various excited states appear to have
characteristic TRIR spectra. We assign the first of these to [4Cr(TMP)2(1dppz)]3+ and with
the aid of the TRIR spectrum supported by DFT calculations assign
the next state to the [4Cr(TMP)2(3dppz)]3+ species formed by intersystem crossing. It should
also be noted that LMCT states are expected to lie energetically between
the LC states and the lowest lying 2MC state. Although
we have no definitive evidence for such LMCT states, it is possible
that the species decaying with a lifetime of 4 ns is such an excited
state. The identification of the LC upper excited states is highly
significant, as until now discussion of the dynamics of Chromium polypyridyl
complexes in terms of photocatalysis[26,64] and DNA photodamage[32,36,51] has been dominated by the role
of the 2MC state and the ability to tune its energy through
ligand substitution.[65]The strong
binding affinity of 1 for DNA places the
intercalating dppz ligand in direct contact with the base pair (see Figure a). Critically,
this now allows the relatively short-lived LC dppz excited state ([4Cr(TMP)2(1dppz)]3+) to participate
in electron transfer processes (see Figure b–c). The absorption spectrum indicates
that this LC state lies ca. 120 kJ mol–1 higher in energy than the 2MC state, for which the excited
state reduction potential, E0(*Cr3+/Cr2+) = 1.39 V, has been reported. Thus, a value
of E0(*Cr3+/Cr2+) ca. 2.6 V may be calculated for the LC species.[32] When bound to guanine-containing DNA, we propose that the
initially formed excited state, i.e. [4Cr(TMP)2(1dppz)]3+, undergoes subpicosecond electron
transfer with the nucleobase to form [4Cr(TMP)2(dppz•–)]2+/(G•+C). This species has a distinct TRIR spectrum in which the metal
complex is associated with the GC base pair, as evidenced by the strong
nucleobase bleaching (Figure ). These results are similar to what we previously reported
for rac-[Cr(phen)2(dppz)]3+, which also undergoes rapid quenching.[35] In the case of DNA containing only AT base pairs, a striking observation
is that excitation of 1 produces a product having a characteristic
absorption band at ca. 1708 cm–1 and a lifetime
of 27 ps (Figure ).
DFT calculations indicate that such an absorption band is expected
for a thymine HB to an adenine radical cation (AT) in a WC base pair (Figure ).
Figure 11
Schematic example of
expected changes in electron density for Λ-1
intercalated into a (a) base-pair step upon (b) formation of the LC
excited state and (c) subsequent electron transfer. Orange = LC excited
state, red = oxidized purine, blue = reduced dppz ligand.
Schematic example of
expected changes in electron density for Λ-1
intercalated into a (a) base-pair step upon (b) formation of the LC
excited state and (c) subsequent electron transfer. Orange = LC excited
state, red = oxidized purine, blue = reduced dppz ligand.In mixed DNA sequences the TRIR spectra of both Λ-1 and Δ-1 indicate the formation of a short-lived
reversible electron transfer photoproduct having a strong transient
band observed at ca. 1706 cm–1 (Figure and Figure S17). Critically, the bleaches predominantly associated with
the GC base pairs are taken to report on the site of photo-oxidation.
The recovery to the ground state occurs rapidly (<100 ps) with
similar biexponential kinetics, which may arise due to the complex
being in different binding sites or in different orientations (Figure ).[9,66] This is interesting as previous equilibrium dialysis of Λ-1 with DNA demonstrated a marked preference for alternating
AT over alternating GC base sequences.[32] Furthermore, as ST-DNA is a heterogeneous system with up to 10 distinct
base pair steps and 42% GC composition, some photo-oxidation would
be expected to occur at sites containing AT and GC steps. The observation
in ST-DNA of GC as the dominant site of photo-oxidation may be explained
by the fact that even if the complex intercalates at an AT/AT or a
TA/TA base pair step, charge transfer by hole migration to guanine
would be a favored process.[67−69] Importantly, by 2 ps in natural
DNA oxidation is localized predominantly at GC sites indicating that
any hole transfer is very rapid and is found to occur for both enantiomers.Our results demonstrate the photo-oxidizing behavior of 1 to be strikingly different from that of other metal complexes which
are known to cause one-electron-oxidation of DNA and where transient
spectroscopic experiments have been carried out. Notably, the electron
transfer dynamics of 1 are extremely fast, occurring
within 100 ps in mixed DNA. This contrasts with the behavior of the
extensively studied [Ru(TAP)2(dppz)]2+ complex
where electron transfer from guanine to generate the G•+ radical cation species proceeds with a forward rate of about 1/500
ps and back reaction with lifetimes between 5 and 20 ns depending
on the sequence.[10,40,44,70] The slower dynamics for [Ru(TAP)2(dppz)]2+ can be explained by electron transfer occurring
from guanine to the Ru(III) center of the MLCT state which is more
removed from the GC base pair than is the case for 1 and
by the back reaction between the oxidized guanine and the reduced
ancillary TAP ligand, which are relatively far apart and orthogonal
to each other.In a detailed study of intercalating rhenium
carbonyl compounds,
Barton, Vlcek and co-workers investigated a tethered [Re(CO)3(dppz)py]+ derivative bound to oligonucleotides containing
either only GC or only AT base pairs as well as mixed sequences.[9] They concluded that oxidation of guanine by the
excited state could only occur if the metal complex was intercalated
at a G-C basepair. Indirect evidence for very rapid electron transfer
to guanine from LC and MLCT states was reported. However, significantly
they showed that charge migration through the DNA basepair stacks
could occur. George, Kelly and co-workers similarly reported that
with [Re(CO)3(F2dppz)py]+ 66% underwent
subpicosecond electron transfer and 34% with a lifetime of 34 ps when
the complex was bound to double-stranded polydGC.[7] As with 1 these studies both propose a role
for LC states oxidizing guanine on a subpicosecond time scale, but
unlike in our case being unable to oxidize adenine. This is presumably
because the redox potential of the excited state of the rhenium complexes
is insufficient to do so. With 1, as was pointed out
earlier, the LC is predicted to be a very strong oxidizing agent (estimated
(E0(*Cr3+/Cr2+)
ca. 2.6 V).Evidence of adenine photo-oxidation by transition
metal complexes
is extremely rare. An exceptional study reported the photo-oxidation
of adenine by the MLCT state of the highly oxidizing Ru(tap)(hat)22+ and Ru(hat)32+ (HAT =
1,4,5,8,9,12-hexaazatriphenylene) when bound to poly(dA-dT) (albeit
bound more weakly than dppz complexes), observed indirectly by quenching
of emission of these complexes.[71] Yet,
until now the direct observation of sensitized adenine photooxidation
to generate the adenine radical cation has not been observed. In this
study our combined TRIR and DFT characterization has allowed the identification
of the elusive adenine radical cation (AT), which is formed due to the proximity of the
dppz LC upper excited state of 1 when intercalated in
DNA.
Conclusion
This study reveals the key role of a second and
more potent LC
oxidizing state of the chromium polypyridyl complex 1 in the mechanism of DNA photodamage. While the 2MC state
is expected to participate in photo-oxidation observed in the case
of diffusional quenching, when 1 is intercalated the
preorganization of the dppz ligand adjacent to Watson Crick base pairs
facilitates photo-oxidation to be dominated by the LC state, circumventing
the 2MC state. TRIR and DFT reveal that, when 1 is bound exclusively to AT ODNs, photoexcitation generates the radical
adenine cation (AT). Furthermore, in mixed DNA systems binding at an AT site
likely leads to hole migration to form the guanine radical cation.
In contrast to other systems, this enhanced photoactivity, irrespective
of binding site, contributes to the significant formation of the guanine
radical cation in natural DNA. These observations have important implications
for the application of chromium polypyridyl complexes as both photocatalysts
and nucleic acid targeting therapeutics. Our increased understanding
of the role of ligands in transition-metal-mediated catalysis[72] has placed focus on chromium’s rich redox
chemistry.[73] Preorganization of the substrate
could be used to enhance the photocatalytic activity of these complexes
in radical cation mediated reactions.[26] Ruthenium polypyridyl complexes are actively pursued as antimicrobial
agents;[74,75] however, the combined photoactivity and
affinity of 1 toward AT-rich DNA opens the possibility
of improved activity through targeting AT-rich repeated sequences
of bacterial replicons.[76] Additionally,
as an earth-abundant element, chromium complexes are economical and
sustainable constituents for these applications. It is clear that
the photochemistry of chromium polypyridyl complexes allows them to
boldly go where no complexes have gone before.
Experimental
Section
5-Guanosine monophosphate (GMP) and deoxy adenosine
monophosphate
(dAMP) were supplied by Sigma-Aldrich. 5′-GCGCGCGCGC-3′
(84 400 M–1 cm–1), 5′-CGCGAATTCGCG-3′
(101 700 M–1 cm–1), 5′-CGCAAATTTGCG-3′
(112 500 M–1 cm–1), 5′-ATTATTATTATATTA-3′
(158 300 M–1 cm–1), and
5′-(TAATATAATAATAAT)-3′ (167 200 M–1 cm–1) were synthesized by Eurogentec
(Liege, Belgium) and obtained in HPLC purified form. Oligodeoxynucleotide
concentrations were determined spectrophotometrically using the single-strand
extinction coefficients at 260 nm shown in parentheses and made up
in D2O in the presence of 50 mM potassium phosphate buffer,
pH 7. Solution samples for transient spectroscopy measurements were
prepared by dropping a known volume of solution (25–35 μL)
between two CaF2 (25 mm diameter) windows (Crystran Ltd.,
UK), separated by a Teflon spacer of 50 μm path length, in a
demountable solution IR cell (Harrick Scientific Products Inc., New
York).[Cr(TMP)2(dppz)]2+ (1) was synthesized
using previously reported methods.[32] The
chiral resolution of 1 was achieved by cation exchange
chromatography following a method described by Vasudevan et al.[33] First, 40 mg of 1 as PF6– salt were exchanged to the chloride form by stirring
a methanolic solution over Dowex 1X8-200 for 2 h, followed by evaporation
to dryness. The racemic mixture of the complex was dissolved in water
(1 mL) and loaded onto a sephadex C-25 stationary phase with a (−)-O,O′-dibenzoyl-l-tartrate chiral eluent.
The column was run at a flow rate of 2 mL/min. The resolved bands
were collected into several centrifuge tubes (12 fractions, 5 mL each).
The two separate fractions were immediately converted from the water-soluble
tartrate salts to the PF6– salts by addition
of ammonium hexafluorophosphate (NH4PF6). This was done to prevent racemization, which has been observed
for solutions of the tartrate salts. The yellow precipitate was collected
by centrifugation (3000 rpm; 3 min) and washed with water (0.5 mL).
Then, lambda and delta enantiomers were dissolved in a minimum volume
of acetone and stirred at room temperature using a chloride anion
exchange resin (Dowex 1X8-200) in methanol for 2 h. After that period,
the solutions were filtered and evaporated to dryness. The concentration
of the complex was determined using the molar extinction coefficient
16 600 M–1 cm–1 at 360
nm.[32]
Instrumental Methods
UV/vis absorption
spectra were
recorded on a Varian Cary 200 spectrophotometer. Steady-state luminescence
spectra were recorded on a Varian Cary Eclipse. Circular dichroism
measurements were recorded on a JASCO J180. Infrared spectra were
recorded on a Nicolet Avatar FT-IR spectrometer or Varian 3100 FT-IR
spectrometer fitted with a Universal ATR Sampling Accessory for solid
samples or N2 flushed liquid samples between CaF2 plates with an optical path length of 100 or 150 μm and at
a resolution of 4 cm–1 and 256 scans.
Computational
Methods
Metal Complex
All quantum chemical calculations on
the metal complexes were performed using Gaussian 16 (Revision B.01)
as implemented at the Irish Centre for High-End Computing.[77] Molecular structures were optimized to tight
convergence criteria. The molecular structure and density maps were
visualized using GaussView 6,[78] while fragment
contributions to orbitals were extracted using AOMix.[79,80] The unrestricted B3LYP hybrid Density Functional Theory (DFT) was
used,[81,82] coupled to the double-ζ quality LanL2DZ
basis set.[83] A similar approach proved
successful in characterizing the nature of excited states and the
normal modes of related ruthenium systems.[41,55] At each optimization, the Hessian matrix was found to contain no
negative elements, which confirms that the structures sit in a minimum
on the potential energy hypersurface. Corrections for solvent dielectric
(water) were applied in these calculations using the Polarizable Continuum
Model (PCM) and the integral equation formalism variant (IEFPCM).[84]
Ade•+ in AT Steps Containing
Adenine Cation
Several models have been used for describing
duplexes containing
the AT step (SI). Their “neutral”
and cationic form were optimized, in which one of the bases was in
its cationic form. All the calculations have been performed at the
DFT level, using the M052X[85] functional
combined with the 6-31G(d) basis set. Solvent effects were also considered
using PCM[86,87] and in some cases by inclusion of specific
water molecules (SI). Harmonic spectra
were built by inclusion of a broadening at each transition with a
Gaussian of h.w.h.m = 10 cm–1 and uniformly scaled
by a factor of 0.955. This procedure has been satisfactorily applied
to model the spectral properties of oligonucleotides (including their
IR spectra)[58,88,89] and the behavior of adenine cation within DNA, providing IR spectra
in good agreement with their experimental counterparts.[90−92] Test calculations were also performed on a simpler model, i.e. 9methyl-A:1methyl-T
dimer in a WC arrangement (see SI), by
varying the density functional and/or the basis set. The computed
difference spectra are fully consistent with those obtained on larger
systems with M052X/6-31G(d). Our conclusions are thus solid with respect
to the adopted computational model, functional and basis set.
TRIR Measurements Using LIFEtime Apparatus
TRIR measurements
were performed using the LIFEtime apparatus at the Central Laser Facility.[93,94] Briefly, a dual Pharos regenerative amplifier system (Light Conversion)
was used to generate 1030 nm synchronized probe (100 kHz, 50 μJ,
180 fs) and pump (0.01–50 kHz, 150 mJ, 260 fs) pulses. The
probe laser was used to drive two OPAs (Orpheus-ONE, Light Conversion),
which generated tunable mid-IR probe light via successive steps of
optical parametric generation in BBO, KTA and difference frequency
generation in GaSe. The two independently tunable mid-IR probe beams
were focused through the sample with <70 μm spot sizes (fwhm)
and dispersed onto two separate 128 pixel MCT array detectors (IR
Associates). The second harmonic of the pump laser (515 nm) was used
to pump a BBO-based OPA (Orpheus-HP, Light Conversion), generating
373–400 nm pump light from the second harmonic of the signal.
The 373–400 nm pump light was delivered to the sample via a
1.2 m length two-pass delay stage (Newport) and focused through the
sample with a spot size of 150 μm fwhm (pump–probe polarization
“pp” was set at magic angle). Pump–probe delays
were set using a combination of the delay stage (0–16 ns) and
seeding of the two regenerative amplifiers with different seed pulses
from their common oscillator (giving delays in 12 ns out to 10 ms).
In the present experiments, the samples were observed to recover on
a μs time scale, and so 50 kHz pumping in combination with rastering
of the sample was used. The 400 nm pump energy was 200 nJ.
ps-TA
(373 nm) and ns-TA (355 nm) Measurements
The
TA experiments were performed on ULTRA apparatus at the Central Laser
Facility.[94] For the ps-TA measurements,
part of the titanium sapphire laser output beam was used to generate
a white light continuum (WLC) in a CaF2 plate. The crystal
plate was continuously rastered to avoid color center formation and
to improve stability in the probe. The WLC was dispersed through the
grating monochromator and detected using a linear silicon array (Quantum
Detectors). In front of the monochromator, a long-pass filter was
placed in order to remove scatter from the excitation beam. The 373
nm pump beam (pulse length ca. 50 fs) was provided by the OPA (TOPAS,
Light Conversion) pumped with the fundamental beam of the 10 kHz titanium
sapphire laser. For ns-TA, the same setup was used; however, the pump
beam was provided by the Q-switched ns laser (InnoLas, pulse length
1 ns) electronically synchronized with the main 10 kHz titanium sapphire
amplifier. The third harmonic output (355 nm) of that ns laser was
used to excite the samples. The polarization of the pump pulses at
the sample was at the magic angle relative to the probe, with an energy
of 1 μJ and a spot size of ca. 100–150 μm. The
spectra were calibrated using five band-pass filters.
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