Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2004
SUPPLEMENTARY MATERIAL
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high
DNA affinity
Janice Aldrich-Wrighta*, Craig Brodiea, Edith C. Glazerb, Nathan W. Luedtkeb, Lev
Elson-Schwabb and Yitzhak Torb
a
School of Science, Food and Horticulture, College of Science, Technology and Environment,
University of Western Sydney, Penrith South, NSW, 1797, Australia. Fax: (+61) 246203025;
Tel: (+61) 246203218; E-mail: J.Aldrich-Wright@uws.edu.au
b
Department of Chemistry and Biochemistry, 0358, University of California, San Diego, La
Jolla, CA 92093-0358, U.S.A.
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high DNA affinity
Aldrich-Wright, Brodie, Glazer, Luedtke, Elson-Schwab & Tor
1
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2004
Method for the Determination of Equilibrium Binding Constants and an Example
Spectroscopic data from each experiment
Using the information gained from the emission spectra and utilising the methods of McGee and von Hippel27
(for the monomer) and Roger and Nordén26 (for the dimers), the binding constants for each of the compounds were
determined. A way to measure the binding strength between two molecules is to determine the equilibrium binding
constant between the free metal complex, empty binding site and bound metal complex. The relationship is a ratio
of the concentration of the bound metal complex (MCb), concentration of the free metal complex (MCf) and the
free DNA site concentration (DNAf) as shown in Equation 1. For this experiment the metal concentration was kept
constant (MCtot) while the DNA concentration (DNAtot) was varied with the addition of aliquots of DNA. If the binding event
is independent (that is no cooperative or non-cooperative binding) then equation 2 shows the relationship between varying
DNAtot concentration and the change in emission ().26 The Rodger and Nordén26 method has the advantage of not requiring
low or high loading data. By plotting the x and y values of equations 3 and 4, a linear relationship with a slope of MC tot/ and a
y-intercept of nis produced Where n is the number of binding sites (in base pairs) and i is a constant that varies with
wavelength. is derived from the observed spectrum as a consequence of changes the proportion of metal complex bound
(MCb) as represented in equation 5. The concentration of free metal complex (MCf), (the total metal complex (MCtot)
- the metal complex bound (MCb)) is determined for each concentration of complex added and is then used to form
a Scatchard plot of r versus r/MCf, (r and r/MCf are defined below). The slope = -Kb and the y-intercept = Kb/n are
obtained from the plot (equation 6). When the a Scatchard plot is not linear the Kb and n are obtained from the
McGee / von Hippel equation (7).
Kb 
DNA  DNA
 j
k
tot
k
j
tot
k
 DNAtot
DNAtotj


k
j
 
x
k   j



(1)
MCb
DNA f MC f
MC tot

k
 DNAtot
DNAtotj


k
j
 

k   j












  n



k
DNAtot
 DNAtotj
y
k   j
Lb  
r
K
 b  rK b
MC f
n
where
r
MC bk
r
DNA k
(2)
(3 & 4)
(5)
and
d
 1  nr 
 K b 1  nr 

MC f
 n  (1  n)r 
r
MC f

MC bk DNA
MC kf
(6)
n 1
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high DNA affinity
Aldrich-Wright, Brodie, Glazer, Luedtke, Elson-Schwab & Tor
(7)
2
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2004
Binding data determined for [Ru(dpq)2(phen)]Cl2 [1.23 x 10-6] bound to Calf Thymus DNA in 10 mM aqueous
pH 7.1 phosphate buffer and 100 mM NaCl, 1 mM EDTA. Emission plot and response curve is at the top with the
data below.
30
[Ru(dpq)2(phen)]2+ titrated with CT-DNA
18
Emission at 606 nm
16
25
12
10
Response Curve for the titration of [Ru(dpq)2(phen)[2+
8
6
4
20
Emission intensity
14
2
0
0.0E+00
4.0E-05
8.0E-05
1.2E-04
1.6E-04
[DNA]
15
10
5
0
500
550
600
650
700
750
800
Wavelength (nm)
4.16 x 10-8
[Metal] =
[DNA/bp]
[DNA]/[Ru]
0.00E+00
2.59E-07
7.75E-07
1.29E-06
1.81E-06
2.32E-06
2.83E-06
3.35E-06
4.37E-06
5.39E-06
6.41E-06
7.43E-06
8.44E-06
9.96E-06
1.15E-05
1.40E-05
1.65E-05
1.89E-05
2.14E-05
2.38E-05
2.62E-05
2.98E-05
3.34E-05
3.81E-05
4.28E-05
4.96E-05
5.86E-05
7.16E-05
8.42E-05
9.63E-05
1.16E-04
1.34E-04
0
6
19
31
44
56
68
81
106
131
155
180
205
243
280
342
404
466
529
591
653
746
839
964
1088
1275
1523
1896
2270
2643
3264
3886
[DNA/bp] stock solution = 7.76 x 10-4
Emission Measured
Max 606 nm
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high DNA affinity
Aldrich-Wright, Brodie, Glazer, Luedtke, Elson-Schwab & Tor
8.89
9.12
9.69
10.13
10.43
10.85
11.29
11.60
12.28
12.67
13.10
13.64
14.16
14.77
15.45
16.18
17.13
17.80
18.25
18.82
19.39
20.28
20.64
21.52
22.00
22.55
23.18
23.96
24.46
24.99
25.28
25.08
3
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2004
Binding data determined for [Ru(dpq)2(phen-4-SOS)]Cl2 [8.72 x 10-7] bound to Calf Thymus DNA in 10 mM
aqueous pH 7.1 phosphate buffer and 100 mM NaCl, 1 mM EDTA. Emission plot and response curve is at the top
with the data below.
80
70
60
Corrected Emission at 605 nm
60
4-Monomer titrated with CT-DNA
50
40
0= [DNA]/[4 Monomer +Linker]
0.4
30
Response Curve for the DNA titration of the 4-Monomer + linker
20
0.6
10
0.9
1.2
0
Emission Intensity
0.E+00
1.E-05
2.E-05
3.E-05
[DNA]
4.E-05
5.E-05
1.3
6.E-05
1.5
50
1.8
2.3
4
40
6
11
20
30
39
57
76
20
10
0
500
600
700
Wavelength (nm)
8.72 x 10-7
[Metal] =
[DNA/bp]
0.00E+00
3.82E-07
5.09E-07
6.36E-07
7.63E-07
1.02E-06
1.14E-06
1.27E-06
1.52E-06
2.03E-06
3.04E-06
5.03E-06
8.97E-06
1.66E-05
3.10E-05
4.42E-05
5.66E-05
[DNA/bp] stock solution =
3.85 x 10-4
Emission Measured
[DNA]/[DIMER]
Max 603 nm
0.0
25.09
0.4
26.58
0.6
27.94
0.7
32.00
0.9
30.02
1.2
31.36
1.3
32.57
1.5
33.11
1.8
33.95
2.3
36.12
4
39.45
6
43.46
11
51.47
20
59.70
39
69.86
57
73.98
76
72.51
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high DNA affinity
Aldrich-Wright, Brodie, Glazer, Luedtke, Elson-Schwab & Tor
4
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2004
Binding data determined for [{Ru(dpq)2}2(phen-3-SOS-3-phen)]Cl4 [4.99 x 10-8] bound to Calf Thymus DNA in
10 mM aqueous pH 7.1 phosphate buffer and 100 mM NaCl, 1 mM EDTA. Emission plot and response curve is at
the top with the data below.
3-3 Dimer titrated with CT-DNA
18
40
30
Corrected Emission at 603 nm
16
14
12
1
8
3
6
4
5
2
7
0
0.E+00
Emission Intensity
0 = [DNA]/ [DIMER]
Response Curve for the DNA titration of the 3-3 dimer
10
9
1.E-06
2.E-06
3.E-06
4.E-06
5.E-06
11
[DNA]
13
15
17
20
19
21
23
27
35
51
10
83
0
500
600
700
Wavelength (nm)
4.99 x 10-8
[Metal] =
[DNA/bp]
0.00E+00
5.01E-08
1.50E-07
2.50E-07
3.50E-07
4.50E-07
5.50E-07
6.50E-07
7.49E-07
8.49E-07
9.49E-07
1.05E-06
1.15E-06
1.35E-06
1.74E-06
2.53E-06
4.10E-06
[DNA/bp] stock solution =
3.01 x 10-4
Emission Measured
[DNA]/[DIMER]
Max 603 nm
0
24.43
1
25.98
3
28.76
5
31.19
7
33.00
9
34.01
11
34.70
13
35.53
15
36.65
17
36.41
19
36.85
21
37.35
23
37.72
27
37.88
35
38.74
51
39.29
83
39.73
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high DNA affinity
Aldrich-Wright, Brodie, Glazer, Luedtke, Elson-Schwab & Tor
5
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2004
Binding data determined for [{Ru(dpq)2}2(phen-4-SOS-4-phen)]Cl4 [3.35 x 10-8] bound to Calf Thymus DNA in
10 mM aqueous pH 7.1 phosphate buffer and 100 mM NaCl, 1 mM EDTA. Emission plot and response curve is at
the top with the data below.
35
Emission Intensity at 610 nm
30
25
Corrected Emission at 610 nm
20
4-4 dimer titrated with CT-DNA
10
Response Curve for the DNA titration of the 4,4'-dimer
0 = [DNA]/[DIMER]
1
3
0
0.E+00
2.E-06
4.E-06
4
6.E-06
[DNA]
6
20
7
9
10
15
12
13
15
10
18
24
36
5
60
0
500
600
700
[DNA]
8.57 x 10-8
[Metal] =
[DNA/bp]
0.00E+00
1.28E-07
2.56E-07
3.85E-07
5.13E-07
6.41E-07
7.68E-07
8.96E-07
1.02E-06
1.15E-06
1.28E-06
1.53E-06
2.04E-06
3.06E-06
5.07E-06
[DNA/bp] stock solution =
3.85 x 10-4
Emission Measured
[DNA]/[Dimer]
Max 610 nm
0
13.91
1
16.98
3
19.75
4
22.24
6
23.96
7
25.04
9
26.21
10
26.98
12
27.77
13
28.36
15
28.64
18
29.25
24
29.80
36
30.80
60
31.54
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high DNA affinity
Aldrich-Wright, Brodie, Glazer, Luedtke, Elson-Schwab & Tor
6
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2004
Binding data determined for [{Ru(dpq)2}2(phen-SOS-5-phen)]Cl4 [2.53 x 10-8] bound to Calf Thymus DNA in 10
mM aqueous pH 7.1 phosphate buffer and 100 mM NaCl, 1 mM EDTA. Emission plot and response curve is at the
top with the data below.
25
Corrected Emission at 602 nm
40
5-5 Dimer titrated with CT-DNA
20
0 = [DNA]/[dimer]
15
Response Curve for the DNA titration of the 5,5'-dimer
5
10
10
15
5
20
30
Emission Intensity
0
0.0E+00
1.0E-06
2.0E-06
3.0E-06
4.0E-06
5.0E-06
25
6.0E-06
30
[DNA]
35
40
45
50
20
60
80
120
200
10
0
500
600
700
Wavelength (nm)
2.53 x 10-8
[Metal] =
[DNA/bp]
0
1.28E-07
2.56E-07
3.85E-07
5.13E-07
6.41E-07
7.68E-07
8.96E-07
1.02E-06
1.15E-06
1.28E-06
1.53E-06
2.04E-06
3.06E-06
5.07E-06
[DNA/bp] stock solution =
3.85 x 10-4
Emission Measured
[DNA]/[Dimer]
Max 605 nm
1
20.60
5
25.48
10
28.17
15
30.13
20
31.64
25
33.28
30
34.31
35
35.59
41
36.46
46
37.43
51
37.96
61
38.64
81
39.89
122
40.65
203
41.84
Dinuclear complexes based on [Ru(dpq)2(phen)]2+ with high DNA affinity
Aldrich-Wright, Brodie, Glazer, Luedtke, Elson-Schwab & Tor
7