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 44106 USA

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

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)

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, 11182.

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.

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?

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 OD @266nm Back-to-back measurement

Femtosecond Transient Absorption Experimental Setup

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

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)

UV/UV TA in Adenine DNA Strands

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

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

Excimer Yields of Long-Lived States in Adenine Multimers Hypochromicity@267 nm 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

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.

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