1. 63rd International Symposium on Molecular Spectroscopy
June 16-20, 2008
UV/UV Femtosecond Transient Absorption Spectroscopy of Single-Stranded Adenine Multimers
Charlene Su1, Chris Middleton1, Tomohisa Takaya2,
Carlos E. Crespo-Hernández3 and Bern Kohler1
1Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
2Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan
3Department of Chemistry, Case Western Reserve University, Cleveland, OH USA

2. DNA Bases vs. UV Light
The nucleic acid bases are the primary UV chromophores of DNA/RNA.

3. Adenine Multimers poly(rA) (rA)2 dAMP poly(dA) Adenine AMP Ado
(Poly(riboadenylic) acid)
(rA)2 H
dAMP
(Deoxyadenosine monophosphate)
poly(dA)
(Poly(2’-deoxyriboadenylic) acid)
Adenine
AMP
(Adenosine monophosphate)
Ado
(Adenosine)

4. Electronic energy relaxation depends on the base stacking of the adenine homopolymers
AMP
Poly(rA)
Poly(dA)
Poly(rA)
AMP
Poly(rA)
Crespo-Hernández, Cohen, and Kohler, J. Phys. Chem. B, 2004, 108,

5. DNA Photophysical Pathway
SFC
AMP
Excimer
(rA)n or (dA)n IC VC Hn
(dA)18
Crespo-Hernández, Cohen, and Kohler, Nature, 2005, 436, 1141.

6. Base Stacking vs. Excimer State
Base stacking highly correlates with the excimer formation.
What is the minimum number of nucleic acids in a strand to form an excimer state?
How does the number of nucleic acids in a strand affect the excimer yield?

7. Materials and Methods AMP RNA multimers (rA)2 (rA)4 poly(rA)
DNA multimers
(dA)4
(dA)18
poly(dA)
Femtosecond Transient Absorption
Pump @ 266 nm
Probe @ 250 nm
Concentration = 1
Back-to-back measurement

8. Femtosecond Transient Absorption Experimental Setup

9. UV/UV TA in AMP, (rA)4, and (dA)4

10. UV/UV TA in Adenine RNA Strands
What is the minimum number of nucleic acids in a strand to form an excimer state?
TWO
Takaya, Su, de La Harpe, Crespo-Hernández and Kohler, PNAS, 2008(in press)

11. UV/UV TA in Adenine DNA Strands

12. Global Fitting f(t)= A1e-t/t1 + A2 f(t)= A1e-t/t1 + A2e-t/t2 +A3 AMP
Multimer 1
Multimer 2

13. Method to Estimate Excimer Yields
pump wavelength
the amplitude of the fast component in the multimer
the amplitude of the fast component in the monomer
fe: h:
A1multi:
A1mono:

14. Excimer Yields of Long-Lived States in Adenine Multimersnm
Excimer Yield
(rA)2
0.137
0.32 ± 0.01
(rA)4
0.245
0.50 ± 0.02
polyA
0.367
0.57 ± 0.05
(dA)4
0.185
0.61 ± 0.02
(dA)18
0.258
0.83 ± 0.04
polydA
0.410
0.76 ± 0.06

15. Conclusions
The UV-induced photodynamics of single-stranded adenine multimers have been investigated using femtosecond transient absorption technique.
All excited adenine multimers have a short-lived component caused by vibrational cooling to the electronic ground state and a long-lived component due to the decay of excimer state.
The amplitude of the bleach signal arising from excimer states increases with the number of adenine bases in a tract, while the lifetime remains constant.
Higher excimer yields are observed in DNA than in RNA tracts, which is attributed to the higher degree of base stacking in the DNA tracts.

16. Acknowledgment Professor Bern Kohler Dr. Carlos E. Crespo-Hernández
Dr. Chris Middleton
Dr. Tomohisa Takaya
Funding:
Instrumentation: