of 16
Crystal structure of
Δ
-Ru(bpy)
2
dppz
2+
bound to mismatched DNA
reveals side-by-side metalloinsertion and intercalation
Hang Song
,
Jens T. Kaiser
, and
Jacqueline K. Barton
*
Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, CA
91125
Abstract
DNA mismatches represent a novel target in developing diagnostics and therapeutics for cancer,
since deficiencies in DNA-mismatch repair (MMR) are implicated in many cancers and cells that
are MMR-deficient show a high frequency of mismatches. We use metal complexes with bulky
intercalating ligands serve as probes for DNA mismatches. Here, we report the high resolution
(0.92 Å) crystal structure of the ruthenium ‘light switch’ complex
Δ
-Ru(bpy)
2
dppz
2+
(bpy = 2,2
-
bipyridine and dppz = dipyridophenazine), known to show luminescence on binding to duplex
DNA, bound to both mismatched and well matched sites in the oligonucleotide 5
-
(dCGG
AAATT
ACCG)
2
-3
(underline denotes AA mismatches). Two crystallographically
independent views reveal that the complex binds mismatches through metalloinsertion, where the
dppz inserts into the duplex through the minor groove, ejecting both mispaired adenosines.
Additional ruthenium complexes are intercalated at well-matched sites, creating an array of
complexes in the minor groove stabilized through stacking interactions between bpy ligands and
extruded adenosines. This structure attests to the generality of metalloinsertion and
metallointercalation as DNA binding modes.
Deficiencies in DNA mismatch repair (MMR) have been linked to increased rate of
mutation and several types of cancers.
1-7
Detection of MMR deficiency typically relies on
assessment of markers for microsatellite instability, promoter hypermethylation and/or
immunohistological staining of MMR proteins.
8-10
These methods may not be applicable to
all cancers, and more than one MMR protein needs to be considered. On the other hand, all
forms of MMR deficiency are expected to show elevated levels of DNA mismatches, which
by themselves would be a persistent and universal target for diagnostic agents. Luminescent,
mismatch-targeting small molecules are thus ideally suited to become a direct, fast, and
sensitive detection method for MMR deficiency in biological samples. We have previously
discovered that the metal complex Ru(bpy)
2
dppz
2+
(where bpy = 2,2
-bipyridine and dppz =
dipyrido[3,2-
a
:2
,3
-
c
]phenazine) shows enhanced luminescence in the presence of base
mismatches and abasic sites.
11
Its augmented luminescence sensitivity to mismatches makes
it a promising parent complex for the design of luminescence-based mismatch sensors.
Further development necessitates a thorough structural understanding of the interactions
between the ruthenium complex and DNA. Here, we report the atomic resolution structure
of
Δ
-Ru(bpy)
2
dppz
2+
(
1
) cocrystallized with a 12-mer oligonucleotide containing two
adenosine-adenosine mismatches, and examine in detail the binding interactions between the
metal complex and DNA.
*
To whom correspondence should be addressed at jkbarton@caltech.edu.
AUTHOR CONTRIBUTIONS
J.K.B. and H.S. designed the research. H.S. carried out crystallization and solution luminescence
experiments. J.T.K. and H.S. solved the crystal structure. H.S. and J.K.B. wrote the manuscript.
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.
NIH Public Access
Author Manuscript
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. Author manuscript; available in PMC 2013 August 01.
Published in final edited form as:
Nat Chem
. ; 4(8): 615–620. doi:10.1038/nchem.1375.
NIH-PA Author Manuscript
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Dppz complexes of ruthenium have been widely studied due to their unique photophysical
responses to DNA. Typically, emission from these complexes is extremely weak in water,
but their luminescence is significantly enhanced upon binding to double-stranded DNA,
hence the “light switch” effect.
12
Extensive studies in solution have established that these
complexes bind to DNA by intercalation through the planar dppz ligand.
13-17
Some possible
structures have been put forward through theoretical calculations;
18-19
however, due to the
lack of site-specificity in DNA binding, solution and crystal structures have largely
remained elusive. Although the discovery of the unique photophysical properties of this
class of complexes was made over two decades ago, the first crystal structure of a dppz
complex bound to DNA was not obtained until very recently, but it did not capture dppz
intercalation into a native DNA duplex.
20
Besides binding to well-matched DNA, Ru(bpy)
2
dppz
2+
shows further enhanced
luminescence in the presence of DNA defects such as base mismatches.
11
We have proposed
that the binding of Ru(bpy)
2
dppz
2+
to mismatches occurs by metalloinsertion.
11
This
binding mode has been elucidated in crystal structures of the mismatch-targeting rhodium
complex,
Δ
-Rh(bpy)
2
chrysi
3+
(where chrysi = chrysene-5,6-quinone diimine), bound to an
AC or AA mismatch, as well as in solution NMR studies with a CC mismatch.
21-24
In this
binding mode, the intercalating chrysi ligand inserts into the mismatch site from the minor
groove and extrudes the mispaired bases out of the helix, effectively taking their place in the
base stack. Here we show that in the ruthenium-DNA crystal structure, just like the rhodium
complex, Ru(bpy)
2
dppz
2+
binds to mismatches also through metalloinsertion, the inserting
ligand is dppz. The crystal structure described herein, at 0.92-Å resolution, provides several
independent views of ruthenium binding to DNA through dppz intercalation and insertion,
illustrating the structural basis of the interactions between DNA and the “light switch”
molecule as captured by cocrystallization.
RESULTS AND DISCUSSION
Cocrystallization of
Δ
-Ru(bpy)
2
dppz
2+
with DNA
To elucidate the structural basis for Ru(bpy)
2
dppz
2+
interaction with DNA, we
cocrystallized
Δ
-Ru(bpy)
2
dppz
2+
(
1
) with the 12-mer palindromic DNA sequence,
d(C
1
G
2
G
3
A
4
A
5
A
6
T
7
T
8
A
9
C
10
C
11
G
12
)
2
. This sequence contains two AA mismatches
(underlined) and has been previously cocrystallized with
Δ
-Rh(bpy)
2
chrysi
3+
.
22
We
considered that similar binding of the complex at the mismatched site might yield well
defined crystals. Crystals took longer than two months to appear in the crystallization wells,
however. The metal complex and the oligonucleotide cocrystallized in space group
P
1 (see
Supplementary Table S1 for data collection and refinement statistics). The asymmetric unit
contains one double strand of DNA with five bound ruthenium complexes. The structure, at
atomic resolution, revealed three binding modes of the ruthenium complex: (i)
metalloinsertion at the mismatched sites with ejection of the mispaired adenosines, (ii)
Song et al.
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metallointercalation between well-matched base pairs and (iii) end-capping between two
(crystallographically-related) duplexes (Figure 1).
Metalloinsertion at mismatched sites
At the two destabilized AA mismatches, the metal complex inserts deeply from the minor
groove and fully ejects the mispaired adenosines (Figure 1 and Supplementary Figure S1).
We had proposed that Ru(bpy)
2
dppz
2+
binds to DNA mismatches through insertion from the
minor groove, and that metalloinsertion may be a general binding mode for octahedral metal
complexes bearing planar ligands.
11
Increased luminescence is found with a range of DNA
mismatches, and, as with the Rh complexes, correlates with thermodynamic instability of the
mismatch. Here, consistent with our proposal, the ruthenium complex indeed binds tightly to
both mismatched sites through metalloinsertion, with the dppz ligand stacked between the
two flanking base pairs, effectively replacing the mispaired adenosines in the base stack. All
four ejected adenosines are folded back in the minor groove. They adopt the
syn
conformation and stack with the very ruthenium that is inserted at their respective
mismatched site. An overlay of the two separate metalloinsertion sites shows that the local
geometry of the DNA and the relative orientation of the ruthenium complex are highly
conserved between the two sites (Figure 2). The dppz is inserted in a head-on fashion,
positioned halfway between the phosphate backbones, both phenazine nitrogens are well
protected from solvent access. On the other hand, if we only consider the relative orientation
of the dppz with respect to the base pairs above and below the insertion site, the dppz is
inserted at an angle with respect to the dyad axis of either flanking base pair. Compared to
the chrysi ligand, dppz is narrower and symmetric about its long axis. As a result, while the
DNA minor groove widens significantly in the rhodium structures to accommodate the
sterically expansive and asymmetric chrysi complex,
21,22
it does so to a lesser extent in the
case of the ruthenium complex (Supplementary Figure S2).
Intercalation at matched sites
Of the three remaining ruthenium complexes, two are intercalated between well-matched
base pairs, also through the minor groove. This mode of intercalation, namely from the
minor groove, contrasts what was inferred from NMR and competitive fluorescence studies,
in which we had deduced a major groove preference for metallointercalation;
14,17,25
linear
dichroism studies did, however, suggest minor groove association
15,16
. We note that in this
structure, intercalation occurs in conjunction with stacking interactions between an ancillary
bpy ligand of the intercalating complex and either an extruded adenosine or a bpy ligand
from a neighboring complex. These stacking interactions serve to stabilize the intercalated
complex in the minor groove. These contrasting results indicate that the energetic difference
between intercalation from the major groove versus the minor groove must be small.
Computational studies of dppz complexes intercalated into a dinucleotide step also support
the notion of very small differences in intercalation energetics from the two grooves.
18
In
this intercalative binding mode, the dppz ligand is positioned inside the base stack also in a
head-on fashion. The intercalation of the dppz ligand is so deep that the end most distal from
the ruthenium center protrudes into the major groove. Comparison between the two
independent intercalation sites reveals subtle differences in the relative position of the
complex (Figure 3). In the 5
-A
6
T
7
-3
step, the dppz is right in the middle of the two strands
and intercalated more deeply, with most of the stacking interactions formed between the
central ring of the phenazine portion and the bases. For the 5
-C
1
G
2
-3
step, the dppz is
closer to one strand than the other, and both the distal and the central rings of the phenazine
are involved in stacking.
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Crystal packing
The fifth ruthenium complex is sandwiched between two crystallographically related
duplexes (Figure 4). The last GC base pair becomes a frayed end, with the cytidine and the
guanosine pointing down into the minor and major groove of the next duplex, respectively.
The dppz ligand of the end-capping ruthenium complex effectively replaces this terminal
base pair in the helix, providing an anchor for the next duplex to stack upon.
Crystallographically related duplexes are stacked head to tail, forming parallel long rods in
the crystal lattice (Supplementary Figure S3). Aside from the end-stacking interactions
between consecutive duplexes, mediated by the end-capping metal complex, neighboring
parallel rods do not have detectable contacts with one another.
Local distortions of the oligonucleotide duplex
Throughout the DNA helix, the minor groove is densely populated with alternating metal
complexes and extruded adenosines. The five metal complexes are evenly spaced, binding to
DNA at every two base steps. The four mismatched adenosines are sandwiched between the
five metal complexes, and the last metal complex makes contact with the first one in the
next repeating unit. The DNA maintains its B-form, albeit with some local deviations from
ideal B-form geometry (Table 1 and Supplementary Table S2). The overall structure is
slightly bent toward the major groove, similar to what we have observed in the rhodium
structure with the identical DNA sequence.
22
All base pairs show some degree of unwinding
to accommodate inserted and intercalated complexes (Table 1), as expected, since
unwinding of DNA is usually associated with intercalators.
26-28
Most sugar puckers are
C2
-endo or the closely related C1
-exo (or C3
-exo, Supplementary Table S2), suggesting
that alternating C2
-endo/C3
-endo conformations
26
are not required for intercalation. The
rise is approximately doubled at each ruthenium binding site as the metal complex serves as
an additional base pair in the helix, but interestingly, the rise between native consecutive
base pairs are less than 3.3 Å (Table 1). This compression of the vertical space between
consecutive base pairs may be an indication that stacking between the bpy ligands and
extruded adenosines is a dominating interaction, such that the base pairs between the
intercalation sites have to shorten their rise in order for the adenosines and bpy ligands to
reach each other. The average distance between a bpy and an adenosine is in fact 3.3 Å. This
is consistent with our notion that the adenosine-bpy stacking may be driving ruthenium
intercalation from the minor groove. But importantly, the adenosines are extruded in the first
place because ruthenium complexes are inserted at the mismatched sites, and
metalloinsertion has been generally apparent through the minor groove.
21,22
Comparison with other structures
The first crystal structure of a dppz complex bound to DNA is that of the
λ
-enantiomer of
Ru(TAP)
2
dppz
2+
(TAP = 1,4,5,8-tetraazaphenanthrene) bound to a 10-mer
oligonucleotide.
20
The ruthenium complex is found to bind through semi-intercalation of a
TAP ligand between two GC base pairs, as well as intercalation of the dppz ligand between
a GC and a reverse Watson-Crick-paired terminal AT pair, with the adenine and thymine
coming from symmetry-related strands. Besides having a different ancillary ligand, this
complex is of the opposite chirality of our ruthenium complex. We have demonstrated in our
structure that the
Δ
-isomer intercalates through the dppz ligand between natively well-
matched base pairs, but this mode of binding is absent in the TAP structure. This is
consistent with early solution studies of the binding of intercalative metal complexes to
DNA: the ancillary ligands of the
λ
-isomer would be sterically repelled by the backbone of
right-handed B-form DNA, while the
Δ
-isomer has the correct symmetry to fit in the
grooves.
29
In the TAP structure, the DNA duplex adopts an overall B-form despite large
local distortions, and dppz intercalation occurs only at the interface between two duplexes,
which are positioned perpendicular to each other rather than form a continuous helix. At the
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same time, the semi-intercalation of TAP induces a severe kink in the DNA. For the TAP
ligand, full intercalation from the minor groove may be more difficult for the
λ
configuration. With bpy ligands metalloinsertion is highly favored for the
Δ
-isomer, but
only small enantiomeric discrimination occurs with intercalation.
24
Indeed, the
Δ
-isomer, as
shown in the structure reported herein, binds avidly to the right-handed helix through full
intercalation. We may also compare our structure with that of
Δ
-Rh(Me
2
trien)phi
3+
(Me
2
trien = 2
R
,9
R
-diamino-4,7-diazadecane) intercalated in an 8-mer oligonucleotide.
27
The rhodium structure shows only one complex bound per 8-mer duplex, as opposed to five
ruthenium molecules per 12-mer duplex in our structure. Functional groups were installed
on the rhodium complex to form sequence-specific contacts with the DNA in the major
groove, hence the single-site binding at a specific step in the base stack. The complex
Ru(bpy)
2
dppz
2+
, on the other hand, binds nonspecifically to DNA. Thus, binding at multiple
sites along the duplex is observed in the ruthenium structure. The sequence context of the
intercalation or insertion sites – pyrimidine-purine (5
-C
1
G
2
-3
), pyrimidine-pyrimidine (5
-
T
8
C
10
-3
), purine-purine (5
-G
3
A
5
-3
), and purine-pyrimidine (5
-A
6
T
7
-3
) – also speaks
to the non-specific nature of DNA binding by the ruthenium complex.
Solution luminescence
We measured the solution luminescence of
Δ
-Ru(bpy)
2
dppz
2+
(
1
) bound to the mismatched
oligonucleotide, as well as to a fully complementary 12-mer oligonucleotide
d(CGGTAATTACCG)
2
, in order to determine if the crystal structure reflects binding
preferences in solution. As the AA mismatch-containing duplex has a low melting
temperature of 22°C, the experiments were conducted at 4°C to ensure all DNA strands are
properly hybridized. The luminescence from
Δ
-Ru(bpy)
2
dppz
2+
(
1
) bound to mismatched
DNA is about three times the luminescence with the equivalent 12-mer well-matched duplex
(Figure 5), consistent with previously observed higher sensitivity of Ru(bpy)
2
dppz
2+
luminescence response to mismatched DNA.
To determine the groove preference of ruthenium complex binding, we employed the minor
groove-specific quencher, Cu(phen)
2
2+
,
30,31
to quench the luminescence from the ruthenium
complex (Figure 5). Quenching by paramagnetic Cu(phen)
2
2+
is expected rather than a
direct competition for binding sites; Cu(phen)
2
2+
, a non-specific groove binder, binds
several orders of magnitude more weakly to DNA than the intercalative ruthenium complex.
The luminescence associated with mismatched DNA is significantly quenched (by 34%)
with increasing concentrations of Cu(phen)
2
2+
, while luminescence associated with the
matched sequence is quenched to a much lesser extent (12%). This differential quenching is
consistent with the mismatch-bound ruthenium complexes being located in the minor
groove, but those bound to well-matched DNA are mostly in the major groove. Therefore,
although the crystal structure provides a very detailed picture of metalloinsertion and
metallointercalation in the minor groove, it may not capture intercalation events occurring in
the major groove. Perhaps the inherently dynamic nature of ruthenium intercalation from the
major groove, as reflected in the fast exchange and multiple binding conformations revealed
in NMR studies, hinders the formation of well-packed crystals. Nonetheless, the crystal
structure still provides invaluable insight into intercalation of
Δ
-Ru(bpy)
2
dppz
2+
(
1
) when it
is in the minor groove.
CONCLUSIONS
The structure presented here at 0.92 Å-resolution depicts in detail the versatile binding
modes attainable for octahedral metal complexes bearing an intercalating ligand. It shows
two independent views of metalloinsertion, two of intercalation, and one of end-capping. At
destabilized regions of the DNA, the metal complex binds through metalloinsertion in the
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minor groove, accompanied by extrusion of the mismatched bases. This binding mode was
previously observed with a sterically expansive ligand, but this structure clearly
demonstrates that a narrower ligand such as dppz is equally capable of recognizing
mismatches by metalloinsertion, pointing to the generality of this binding mode. The smaller
size of the dppz ligand allows the ruthenium complex also to bind through classical
intercalation between two consecutive well-matched base pairs. Curiously, intercalated
complexes are located in the minor groove as well, which we hypothesize is stabilized by
extensive ancillary interactions; given some major groove intercalation in solution, binding
from the major and minor groove must be energetically similar. This discrepancy
notwithstanding, the crystal structure attests to the remarkable structural flexibility of DNA
upon high-density ligand binding, illustrates the nuanced binding geometries sampled by a
non-covalently bound small molecule, and highlight the dominance of metalloinsertion as
the preferred binding mode to destabilized regions of DNA. We hope these newly garnered
structural understandings will help guide the development of future generations of metal
complexes as chemical tools and medicinal agents.
METHODS
Materials
[Ru(bpy)
2
dppz]Cl
2
was synthesized according to previously reported procedures.
32
The
enantiomers were separated using a CYCLOBOND I 2000 DMP HPLC column (Sigma) on
a Hewlett-Packard 1100 HPLC, with an isocratic solvent composition of 60/40 (v/v)
CH
3
CN:100 mM KPF
6
(aq). The
Δ
-enantiomer eluted first, followed by the
λ
-isomer. The
assignment of the two fractions was confirmed by circular dichroism.
33
The fractions were
lyophilized and washed with water to remove excess KPF
6
and exchanged for chloride salt
on a QAE anion-exchange column. Oligonucleotides (Integrated DNA Technologies) were
purified by reverse-phase HPLC using a C18 reverse-phase column (Varian) on a Hewlett-
Packard 1100 HPLC. Quantification was performed on a Beckman DU 7400
spectrophotometer.
Crystallization and data collection
Oligonucleotides were incubated with
Δ
-[Ru(bpy)
2
dppz]Cl
2
(
1
) before crystallization.
Subsequent manipulations were performed with minimal exposure of the complex to light.
The crystal was grown from a solution of 1 mM d(C
1
G
2
G
3
A
4
A
5
A
6
T
7
T
8
A
9
C
10
C
11
G
12
)
2
, 2
or 3 mM enantiomerically pure
Δ
-Ru(bpy)
2
dppz
2+
(
1
), 20 mM sodium cacodylate (pH 7.0),
6 mM sperminetetrahydrochloride, 40 mM NaCl or KCl, 10 mM BaCl
2
, and 5% 2-
methyl-2,4-pentanediol (MPD) equilibrated in sitting drops versus a reservoir of 35% MPD
at ambient temperature. The crystals grew in space group
P
1 and unit cell dimensions: a =
24.039 Å
,
b = 24.797 Å, c = 37.521 Å,
α
= 74.669°,
β
= 84.416°, and
γ
= 76.208°
(Supplementary Table S1).
Data were collected from a flash-cooled crystal at 100 K on an R-axis IV image plate using
Cu K
α
radiation produced by a Rigaku RU-H3RHB rotating-anode generator with double-
focusing mirrors and a Ni filter. High-resolution data were subsequently collected from a
different crystal on beamline 12-2 at the Stanford Synchrotron Radiation Laboratory (Menlo
Park, CA,
λ
= 0.7749 Å, 100 K, PILATUS 6M detector). The data were processed with or
XDS
34
, and SCALA from the CCP4 suite of programs.
35
Structure determination and refinement
The structure was determined by single anomalous dispersion phasing using the anomalous
scattering of ruthenium with the Shelxc/d/e suite of programs.
36
Five heavy atoms were
located per asymmetric unit. The model was built in COOT
37
and refined with PHENIX
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version 1.7.
38
The anomalous contribution of ruthenium was taken into account and
alternative conformations of phosphates were included in the refinement. Atomic
displacement factors have been refined anisotropically. Figures were drawn with Pymol.
39
Alignment was performed with LSQMAN.
40
The coordinates and structure factors have
been deposited in RCSB Protein Data Bank (PDB ID: 4E1U).
Steady state fluorescence
Luminescence spectra (excitation wavelength = 440 nm) with emission intensities ranged
from 560 to 800 nm were measured in 40 mM sodium cacodylate (pH 7.0), 80 mM KCl, 20
mM BaCl
2
on an ISS-K2 spectrophotometer at 4°C in aerated solutions. Cu(phen)
2
2+
was
formed in situ using 1:3 CuCl
2
and phenanthroline. Experiments were performed in
triplicate.
Supplementary Material
Refer to Web version on PubMed Central for supplementary material.
Acknowledgments
We thank S. C. Virgil for assistance in the separation of enantiomers, and D. C. Rees and J. A. Hoy for valuable
discussions. We are grateful to the National Institutes of Health (NIH GM33309 to J. K. B.) for their financial
support and the Tobacco-Related Disease Research Program (TRDRP) for a Dissertation Research Award to H. S.
We acknowledge the Gordon and Betty Moore Foundation and Sanofi-Aventis Bioengineering Research Program
at Caltech for support of the X-ray Facility at the Caltech Molecular Observatory. The rotation camera facility at
Stanford Synchrotron Radiation Laboratory is supported by the U.S. Department of Energy and NIH.
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Figure 1.
Structure of
Δ
-Ru(bpy)
2
dppz
2+
(1) bound to the oligonucleotide 5
-
C
1
G
2
G
3
A
4
A
5
A
6
T
7
T
8
A
9
C
10
C
11
G
12
-3
shown in a front view (a) and rotated 90 degrees
around the helix axis. Three DNA-binding modes are observed: (i) metalloinsertion,
whereby the ruthenium complex (red) inserts the dppz ligand into the DNA duplex (gray) at
the mismatched sites through the minor groove, extruding the mispaired adenosines (blue),
(ii) metallointercalation, whereby the complex (green) binds between two well matched base
pairs, and (iii) end-capping, whereby the complex (yellow) stacks with the terminal Watson-
Crick pair of the duplex.
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Figure 2.
Two independent views of metalloinsertion at the mismatched sites. a, Superposition of the
two independent views of metalloinsertion by the ruthenium complex at the mismatched
sites, as viewed from the minor groove (A
4
-A
9
site: ruthenium complex in red and DNA in
gray, A
9
-A
4
site: ruthenium complex in green and DNA in blue). The ruthenium complex
inserts the dppz ligand from the minor groove and extrudes the mismatched adenosines,
which are folded back into the minor groove. The two binding sites were superimposed
using only the DNA backbone atoms (rmsd of 42 atoms = 0.607 Å). b, Superimposed
metalloinsertion sites as viewed down the helical axis.
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Figure 3.
Two independent views of metallointercalation at well-matched sites. a, The ruthenium
complex intercalates at the 5
-C
1
G
2
-3
step through the dppz ligand (Ru in orange, DNA
and bpy from a neighboring ruthenium in blue). b, Metallointercalation at the 5
-A
6
T
7
-3
step (Ru in magenta, DNA in gray).
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Figure 4.
The end-capping complex. The duplex (dark gray) is end-capped by the ruthenium complex
(red), which stacks between an extruded adenosine (blue) and the first complex (yellow) in a
crystallographically related duplex (light gray). The last GC base pair (cytidine in cyan and
guanosine in green) forms a frayed end.
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Figure 5.
Solution luminescence. Plot of integrated emission intensity (
λ
ex
= 440 nm) of 1
μ
M
Δ
-
Ru(bpy)
2
dppz
2+
(1) with increasing concentration of Cu(phen)
2
2+
in the presence of 12-mer
mismatched (AA) and well-matched DNA (TA, 1
μ
M). Error bars indicate standard
deviations in the measurements.
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Table 1
Helical parameters
a
of DNA conformation relating consecutive base pairs.
b
Step
Ru binding
mode
Shift (Å)
Slide (Å)
Rise (Å)
Tilt (°)
Roll (°)
Twist (°)
C
1
/G
2
intercalation
0.1
2.2
6.3
12.5
5.5
18.1
G
2
/G
3
-
0.9
0.3
2.9
−3.0
−5.4
30.4
G
3
/A
5
insertion
0.6
3.5
7.0
5.4
16.6
71.7
A
5
/A
6
-
−0.8
−0.1
3.0
−0.7
−0.7
23.2
A
6
/T
7
intercalation
−0.2
0.6
7.1
−1.7
7.6
23.5
T
7
/T
8
-
0.4
−0.4
2.8
−3.4
6.6
23.6
T
8
/C
10
insertion
−0.9
3.4
7.3
−7.5
9.0
70.2
C
10
/C
11
-
−1.0
−0.3
3.0
3.2
−7.5
23.4
B-DNA
-
−0.1
−0.8
3.3
−1.3
−3.6
36
a
Geometrical relationships between consecutive base pairs: shift, translation into the groove, slide, translation toward the phosphodiester backbone, rise, translation along the helix axis, tilt, rotation about
the pseudo-twofold axis relating the DNA strands, roll, rotation about a vector between the C1
atoms, and twist, rotation about the helix axis.
b
Data were calculated using 3DNA.
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