Direct Chemical Evidence for Charge Transfer between Photoexcited 2-
Aminopurine and Guanine in Duplex DNA
Melanie A. O’Neill, Chikara Dohno and Jacqueline K. Barton
Division of Chemistry and Chemical Engineering
California Institute of Technology,
Pasadena, California 91125
Supporting Information
Figure S-1.
Reverse phase HPLC (C18, 2-14 % acetonitrile in 50 mM ammonium
acetate over 30 minutes) traces profiling the decomposition of
CP
G as a function of
irradiation time (325 nm, ~ 3 mW) for 5
m
M ApAAC
CP
G duplexes in 100 mM sodium
phosphate pH 7. Expanded region shows formation of
HP
G as a function of increasing
irradiation time. These traces are representative of those observed for all Ap/
CP
G
duplexes with the exception of ApC
CP
G and ApA
CP
G for which no photodecomposition
was observed.
Figure S-2
. Fluorescence emission spectra (
l
ex
= 325 nm) of 5
m
M Ap/
CP
G duplexes in
100 mM sodium phosphate pH 7. All duplexes are dramatically less emissive (< 5 %)
than free Ap under the same conditions. The following trends in the relative quenching
of Ap within the DNA duplexes are noted: ApAG >
ApA
CP
G; ApAAA
CP
G > ApA
CP
G;
ApAAAAC
CP
G-A-A mismatch > ApAAAAC
CP
G > ApAAC
CP
G. These are consistent
with the influence of donor (G, or
CP
G) distance and oxidation potential (
CP
G < G),
neighboring bases (purines versus pyrimidines) and nearby mismatches on Ap* emission
intensity.
Figure S-3.
Normalized fluorescence excitation spectra (
l
em
= 370 nm) of Ap and
Ap/
CP
G duplexes. Samples are 5
m
M in 100
mM sodium phosphate pH 7. The long
wavelength band, due to direct excitation of Ap is
redshifted in DNA. The magnitude of
this shift reflects the reduction in solvent exposure of Ap within the duplex. The short
wavelength band is due to energy transfer from the natural DNA bases; stronger stacking
interactions facilitate more efficient energy transfer. Both the relative redshift and the
relative intensity of the energy transfer band increase in the following order: Ap <
ApC
CP
G < ApA
CP
G = ApAG. This indicates that Ap does not sense the substitution of
CP
G for G, and that as with G, stacking interactions of Ap in
CP
G duplexes are stronger
with A than with C.
Table S-1.
Melting temperatures (T
m
) of Ap/
CP
G duplexes (3
m
M in 100 mM sodium
phosphate pH 7) determined by monitoring the change in absorption at 260 nm as a
function of temperature (0.5
o
C/minute). The T
m
corresponds to the maximum
D
A/
D
T.
In duplex 7, the A-A mismatch is at the third A from the 5’-end. Note that duplexes 4-7
have a slightly higher GC content (exchange of one GC for AT pair) than duplexes 1-3
leading to a small increase in duplex stabilization.
Number
Duplex
T
m
(
o
C)
1
ApAG
65
2
ApA
CP
G
64
3
ApAAA
CP
G
65
4
ApC
CP
G
68
5
ApAAC
CP
G
68
6
ApAAAAC
CP
G
68
7
ApAAAAC
CP
G A-A mismatch
65
Figure S-1
HP
G
0
5
10
15
20
25
30
Time (min)
dC
dG
dA
dT
CP
G
Dark
5
mins
h
n
10
mins
h
n
15
min
h
n
30
min
h
n
60
min
h
n
Figure S-2
340
360
380
400
420
440
460
480
500
ApAAC
cp
G
ApA
4
C
cp
G
Intensity (a.u.)
Wavelength (nm)
(b)
340
360
380
400
420
440
460
480
500
ApA
cp
G
ApAAA
cp
G
ApAG
Emission Intensity (a.u.)
Wavelength (nm)
(a)
Figure S-3
260
280
300
320
340
Ap
ApC
cp
G
ApA
CP
G
APAG
Intensity (a.u.)
Wavelength (nm)