0-1. / A. 0-0 band intensity ratio for hairpins 2AT, 2TA and 2AA in phosphate buffer. ... (a) 550 and (b) 660 nm in buffer. ... 450 500 550 600 650 700 750 800.
Electronic Supplementary Material (ESI) for Chemical Science This journal is © The Royal Society of Chemistry 2013
Supporting Information for:
Ground and Excited State Electronic Spectra of Perylenediimide Dimers with Flexible and Rigid Geometries in DNA Conjugates
Prakash P. Neelakandan, Tarek A. Zeidan, Martin McCullagh, George C. Schatz, Josh Vura-Weis, Chul Hoon Kim, Michael R. Wasielewski and Frederick D. Lewis*
S1
Electronic Supplementary Material (ESI) for Chemical Science This journal is © The Royal Society of Chemistry 2013
Chart S1
1.1
a) 0.16
2AT 2TA 2AA
1.0 0.9 0-1
0.15
0-0
0.8
A /A
Absorbance
b)
2AT 2TA 2AA
0.14
0.7 0.6
0.13 0
20
40
60
o
80
100 0
20
40
60
80
0.5 100
o
Temperature ( C)
Temperature ( C)
Fig. S1. (a) UV melting curves monitored at 260 nm and (b) the A0-1/ A0-0 band intensity ratio for hairpins 2AT, 2TA and 2AA in phosphate buffer.
S2
Electronic Supplementary Material (ESI) for Chemical Science This journal is © The Royal Society of Chemistry 2013
-1
x 10 (cm dmol )
6 2AT
2TA
0.4
0.0 0 -0.4
-3
2AA
2TT
-1
x 10 (cm dmol )
-4
2
3
0.6
2
0.3
0.0
-4
0.0
-0.6 -0.3 -1.2 400
500
600
400
500
Wavelength (nm)
600
700
Wavelength (nm)
Fig. S2. Long wavelength region of the CD spectra of the hairpins 2AT, 2TA, 2AA and 2TT in phosphate buffer.
-1
0
A:T (H8)2
-4
1
2
x 10 (cm dmol )
2
-1
-2
-3 200
300
400
500
600
Wavelength (nm)
Fig. S3. Circular dichroism spectra of hairpin dimer (H8)21 and duplex A:T in buffer.
S3
Electronic Supplementary Material (ESI) for Chemical Science This journal is © The Royal Society of Chemistry 2013
2
-1
x 10-4 (cm dmol )
3
b)
a)
Heating Cooling
2 o
5 C
o
95 C
1
0.00
0
-0.05
-0.10
-1
o
-0.15
95 C
-0.20
o
5 C
-2
-0.25
0
20
40
60
80
100
o
Temperature ( C)
-3 200
300
400
500
700 0
600
20
40
60
80
Temperature ( C)
Wavelength (nm)
o
100
Fluorescence Intensity (au)
Fig. S4. (a) Temperature dependent CD spectra for 2AT (ca. 1 M hairpin in 10 mM phosphate buffer with 0.1 M NaCl). (b) Temperature dependence of the 560 nm band intensity. Inset shows derivative of 560 nm heating and cooling curves.
30
a)
20
100
em = 550 nm
b)
em = 660 nm
80 2AT 2TA 2AA 2TT
2AT 2TA 2AA 2TT
60 40
10 20 0 300
350
400
450
500
200
Wavelength (nm)
300
400
500
600
0
Wavelength (nm)
Fig. S5. Fluorescence excitation spectra of the hairpins 2AT, 2TA, 2AA and 2TT monitored at (a) 550 and (b) 660 nm in buffer. The spectra of 2AA and 2TT have been multiplied by a factor of 10 in (a) for clarity.
S4
Electronic Supplementary Material (ESI) for Chemical Science This journal is © The Royal Society of Chemistry 2013
Intensity (a. u.)
1000
2AT, 560 nm
1000 100
1 1000
Intensity (a. u.)
Signal 100 Fit IRF
Signal 100 Fit IRF
10
10
10
10
2AA, 560 nm
2TA, 560 nm
Signal Fit 100 IRF
1
1 1000
2AA, 660 nm
100
1
0
3
Signal Fit IRF 6
Time (ns)
9
1 12
3
6
Time (ns)
2TT, 660 nm Signal Fit IRF
10
Signal Fit IRF 0
1
100
2TA, 660 nm
10
2AT, 660 nm
10
Signal Fit IRF
Signal 1000 Fit IRF
100 100
2TT, 560 nm
9
1 12
10 0
3
6
Time (ns)
9
12
0
3
6
9
12
Time (ns)
Normalized Intensity (au)
Fig. S6. Fluorescence decay profiles of various oligonucleotide conjugates at 560 (top) and 660 nm (bottom) in buffer.
1.0
2AT 0.25 ns 2 ns
0.8 0.6 0.4
2TA 0.2
0.2 ns 1.4 ns
Normalized Intensity (au)
0.0
1.0
2TT
2AA
0.8
0.25 ns 2.0 ns
0.25 ns 2.0 ns
0.6 0.4 0.2 0.0
550
600
650
Wavelength (nm)
700
550
600
650
Wavelength (nm)
700
Fig. S7. Time resolved emission spectra of various oligonucleotides in buffer. Sample concentration and experimental conditions same as for fluorescence lifetime measurements.
S5
2TA
12
45
9 o
5 C
30
o
5 C
6
15
3 o
95 C 0
300
Fluorescence Intensity (au)
F546 / F655
2TA
o
95 C
0.21
o
5 C
2TT
25
2TT
0.18
20
o
95 C
0.15
15
0.12
10 5 0
F549 / F655
Fluorescence Intensity (au)
Electronic Supplementary Material (ESI) for Chemical Science This journal is © The Royal Society of Chemistry 2013
0.09
550
600
650
700
750
0 800
20
40
60
80
100
o
Temperature ( C)
Wavelength (nm)
Fig. S8. (Left) Fluorescence spectra and (right) the ratio of monomer to excimer fluorescence intensities of 2TA and 2TT as a function of temperature in buffer. Bold traces in the middle indicate the fluorescence spectra at 25 °C. Excitation wavelength, 505 nm.
0.04 0.02
A
0.00
0.9 ps 5.8 ps 12.3 ps 23.3 ps 40.3 ps 60.3 ps 103.3 ps
-0.02
605 nm
-0.04
708 nm
-0.06 0
-0.08 450
500
550
600
650
100 200 Time (ps)
700
750
300
800
Wavelength (nm) Fig. S9. Transient absorption spectra of hairpin 1A in TE buffer (20 mM Tris, 2 mM EDTA), pH = 7.4, following excitation with 505 nm, 120 fs laser pulses. Inset: transient absorption kinetics at () 605 nm and at () 708 nm. Nonlinear least-squares fits to the data are also shown (data from Zeidan et al.).2 S6
Electronic Supplementary Material (ESI) for Chemical Science This journal is © The Royal Society of Chemistry 2013
References 1.
2.
M. Hariharan, Y. Zheng, H. Long, T. A. Zeidan, G. C. Schatz, J. Vura-Weis, M. R. Wasielewski, X. B. Zuo, D. M. Tiede and F. D. Lewis, J. Am. Chem. Soc., 2009, 131, 5920-5929. T. A. Zeidan, R. Carmieli, R. F. Kelley, T. M. Wilson, F. D. Lewis and M. R. Wasielewski, J. Am. Chem. Soc., 2008, 130, 13945-13955.
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