Supporting Information
Site
-
specific DNA Photocleavage
by Rhod
ium Intercalators an
alyzed by MALDI
-
TOF Mass Spectrom
etry
Jens Brunne
r and
Jacque
line K. Barton
*
Division
of Chemistry and Chemical Engi
neering
California Institute of Technol
ogy
Pasadena
, California, 91125
jkba
rton@
caltech.edu
S1
1.
Syn
thesis
Scheme S1. Syn
thesis of
[Rh(phen)(chrysi)(bpy3C
)]
3+
[Rh(phe
n)(chrysi)(NH
3
)
2
]
3+
was synt
hesized
in
four
steps from
rhodi
um
trichloride,
phe
nanthol
ine and
5,6
-
chrysenequi
none
, and
purified as described by
Schatzschne
ider and
Barton
[1].
4
-
propi
oni
c
acid
-
4 ́
-
methyl
-
2,2 ́
-
bipyr
idine
(bpy3C
)
[2]
was
then
reacted
with
[Rh(phe
n)(chrysi)(NH
3
)
2
]
3+
in a 50% water, ethanol
mixture by
refl
uxing
it for 20h.
The crude
[Rh(phe
n)(chrysi)(bpy3C
)]
3+
was pur
ified on
a Sepha
dex SP C25
colum
n (eluted with 0.05
-
0.5M
MgC
l
2
) and
the produc
t fractions
were isolated on
a Sep Pak C
18
Cartridge
, washed with copi
ou
s
amount
s of water, and
then eluted from
th
e cartridge
with 50%
acetoni
trile/water, acidified with
0,1%
TFA.
The synt
hesis of [Rh(bpy
)
2
chrysi)]
3+
(
2
) and
[Rh(bpy)
(phi
)
2
]
3+
were as described [3].
R
h
C
l
3
N
N
N
N
R
h
H
N
N
H
H
O
O
3
+
N
N
+
O
T
F
O
T
F
N
N
R
h
T
F
O
T
F
O
3
+
N
H
3
N
H
3
N
N
R
h
H
3
N
H
3
N
3
+
C
F
3
S
O
3
H
N
H
3
3
+
O
O
N
N
O
O
H
3
+
N
H
3
N
H
3
N
N
R
h
H
N
N
H
3
+
3
+
C
l
C
l
N
N
R
h
C
l
C
l
S2
Characterization
of
[Rh(phen)(chrysi)(bpy3C
)]
3+
:
Esi
-
MS:
779
M
+
UV
-
Vis:
2
0
0
3
0
0
4
0
0
5
0
0
6
0
0
7
0
0
0
,
0
0
,
1
0
,
2
0
,
3
0
,
4
Absorption
W
a
v
e
l
e
n
g
t
h
1
H
-
NMR
, D
2
O
:
8
.95 (m, 2H
); 8.83 (m, 1H
); 8.82
(m, 1H
); 8,48 (m, 3H
); 8,31
(d, 1 H); 8,27
(s,
1H
); 8,21 (s, 1H
); 7.99 (m, 2H
); 7.78
(m, 3H
); 7.53 (m, 2H
); 7.41 (m, 1H
); 7.31
(m, 1H
); 3.17
(m, 1H
); 3.00
(m, 1H
); 2.75 (m, 1 H); 2.63 (m, 2H
); 2.42 (m, 2H
); 1
.85
(s, 1H
)
[1]
Schatzschne
ider, U.; Barton, J.
K.
J. Am. Chem. Soc.
2004
,
126
, 8630
-
8631
.
[2]
Terbruegge
n, R. H., Timothy, W. J., Barton, J. K.
Inor
g. Chem.
1998
,
37
, 6874
-
6883
.
[3]
Mürner, H.; Jackson,
B. A.; Barton,
J. K.
Inor
g.
Chem.
1998
,
37
, 3007
-
30
12;
Pyle, A. M.;
Chiang,
M.; Barton, J. K.
Inor
g.
Chem.
1990
,
29
, 4487.
S3
Scheme S2. Syn
thesis of the Rh(III) com
plex mod
ified peptide
Solid pha
se bound
and
protected (arginine was protected as its 2,2,4,6,7
-
pentamethyl
dihydr
o
-
benzofuran
-
5
-
sulfonyl
(Pbf) derivative, lysine as its methyl
trityl (Mtt) derivative) p
eptides
were
pur
chased from
AnaSpec Inc. (San Jose, CA, USA) The acid
-
modi
fied metal com
plex
was
coupl
ed to the free amine of the peptide by
standa
rd HOBT/HBTU activated
coupl
ing.
The
peptides were cleaved from
the resin using
95%
TFA, 2.5% triisopr
opyl
silane and
2.5% water for
3h
at room
temperature. In all cases, the final produc
ts were obt
ained in analytical pur
ity using
a
HP1100
HPLC
system fitted with a C18
-
packed reve
rse pha
se colum
n and
analyzed by
ESI
-
and
Maldi
-
TOF mass spectrom
etry. All conj
uga
tes employe
d
in
this study
were used
as their
correspondi
ng
trifluor
oacetate salts bearing
a full com
plement of count
erions
.
Characterization
of 1:
Maldi
-
TOF
-
MS
: M
calc
: 2157
.38
(M
-
2
H)
+
M
found
: 2157.
66;
M
calc
: 1977.
17
(M
-
Phen
-
2
H)
+
M
found
:
1979.
50;
M
calc
: 1901.
08
(M
-
Chrysi
-
2
H)
+
M
found
: 1903.
48;
M
calc
: 1720.
87
(M
-
Chrysi
-
Phen
-
2
H)
+
M
found
: 1722
.56;
M
calc
: 1620
.96
(M
-
Rh
-
Chrysi
-
Phen
+H)
+
M
found
: 1621
.67
ESI
-
MS:
M
calc
: 947
.83
(M+6T
FA
)
3+
M
found
:
947
.62;
M
calc
: 909
.83
(M+5T
FA)
3+
M
found
:
909
.62;
M
calc
: 653.
62 (M+H+4T
FA)
4+
M
found
:
654
.05;
M
calc
: 625.
11 (M+H
-
3T
FA)
4+
M
found
:
625.
55;
M
calc
:
596.
61
(M+H+2T
FA)
4+
M
found
:
597.
05;
M
calc
: 568
.1 (M+H+TFA)
4+
M
found
:
568.
54
L
y
s
(
M
t
t
)
A
r
g
(
P
b
f
)
8
N
H
2
N
H
H
N
N
H
H
N
N
H
H
N
N
H
O
H
N
O
O
O
O
O
O
H
N
O
H
N
O
H
O
H
2
N
N
H
N
H
N
H
H
2
N
N
H
N
H
H
2
N
N
H
N
H
H
2
N
H
N
H
N
N
H
2
H
N
H
N
N
H
2
H
N
H
N
N
H
2
H
N
H
N
N
H
2
N
H
2
R
N
N
R
h
N
N
N
N
H
H
O
H
O
B
T
/
H
B
T
U
R
R
L
y
s
(
M
t
t
)
A
r
g
(
P
b
f
)
8
N
H
T
F
A
/
T
I
S
/
H
2
O
3
+
R
=
S4
2.
DNA Photocleavage
by
MALDI
-
TOF Mass Spectrom
etry
The seque
nces of the DNAs A and
B are show
n below
. The mismatch is highl
ight
ed in red. The
arrow
marks the cleavage po
sition,
one
base 3 ́
-
shifted from
the mismatched site.
Phot
ocleavage
expe
riments
were performed on
a 20
μl scale with
2 μM
1
(except for light
cont
rol expe
riments
LC which were without
1
), 2 μM
dupl
ex DNA A:
B, 50
mM NaCl, 10
mM NaPi, pH
7, 15
min
irradiation
with a 1000
-
W Oriel Hg/Xe arc lamp (Oriel, Stanfort, CT) between 320
-
440nm
wa
velengt
h
(except for dark cont
rol expe
riments DC which were
carried out
without
irradiation)
.
Mismatched DNA
Matched DNA
Figu
re S1. DNA stran
ds used in the photocleavage
exp
eriments, marked cleavage
site an
d
assign
ed cleavage
prod
ucts for the mismatch selective cleavage
with Rh com
plexes 1 an
d 2.
Masses given are those fou
nd in cleavage
with 2 with numbers indicated as in Figu
re 1.
Masses calculated are for the assign
ed structures. R
1
= 5 ́
-
GCG CCG TCG TC
-
3
́; R
2
= 5 ́
-
ATG TG
-
3 ́, B = Cytosine)
(8)
M/Z = 1789.45
(1790.3)
(6)
M/Z = 3389.95
(3390.2)
(3)
M/Z = 5083.
99
(5084.3)
(1)
M/Z = 5180.58
(5179.4)
(10)
M/Z = 1598.16
(1599.1)
M/Z = 1694.91
(1695.2)
(5)
M/Z = 3486.10
(3486.3)
(4)
M/Z = 3579.22
(3581.4)
O
O
P
O
O
O
O
-
P
O
O
-
O
R
2
R
1
O
O
P
O
O
O
O
-
P
O
O
-
O
R
2
R
1
O
O
O
P
O
O
-
O
R
1
B
B
5
́
O
-
P
O
O
O
H
-
R
2
R
h
,
h
v
3
́
O
-
P
O
O
O
-
R
1
O
B
O
P
O
O
-
O
-
O
O
P
O
O
-
O
R
1
O
+
B
3
́
O
-
P
O
O
O
-
R
1
O
O
O
O
+
B
O
P
O
O
-
O
-
R
2
R
2
5
́
O
-
P
O
O
O
-
R
2
O
O
5
-
M
F
5
-
M
F
A
:
5
́
-
G
C
G
C
C
G
T
C
G
T
C
C
A
T
G
T
G
-
3
́
B
:
3
́
-
C
G
C
G
G
C
A
G
C
A
C
G
T
A
C
A
C
-
5
́
C
:
5
́
-
G
C
G
C
C
G
T
C
G
T
G
C
A
T
G
T
G
-
3
́
B
:
3
́
-
C
G
C
G
G
C
A
G
C
A
C
G
T
A
C
A
C
-
5
́
S5