OSA / UP 2010
ME19.pdf
Ultrafast Dynamics of Phosphate-Water Interactions in Hydrated DNA Łukasz Szyc, Ming Yang, Thomas Elsaesser Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany Email:
[email protected]
Abstract: Interactions between DNA and the surrounding water shell are mapped via the ultrafast response of the asymmetric phosphate stretching vibration AS (PO 2 )-. The water shell serves as the primary heat sink for excess energy.
2010 Optical Society of America
OCIS codes: (320.7150) Ultrafast spectroscopy; (300.6250) Spectroscopy, condensed matter; (300.6340) Spectroscopy, infrared
Interaction of DNA with water is of fundamental relevance for its structural conformation, the local hydrogen bond patterns and the electric shielding of charged groups. Under equilibrium conditions, the ionic phosphate groups in the DNA backbone (Fig. 1a) are major hydration sites, each being hydrated by up to 6 water molecules that directly interact with the charged oxygen atoms [1]. While the residence times of water molecules at DNA hydration sites cover a broad time range from 10 ps up to nanoseconds [2], fluctuations of the long-range Coulomb forces and the local hydrogen bond geometries occur on a much shorter ultrafast time scale. Here, we introduce femtosecond vibrational spectroscopy for mapping phosphate-water interactions of hydrated DNA. The nonequilibrium dynamics of energy exchange between DNA and water and the resulting changes of local hydrogen bonds are studied using the asymmetric stretching vibration AS (PO 2 )- of the phosphate groups as a local probe. In the femtosecond two-color pump-probe experiments [3,4], we either excite AS (PO 2 )- oscillators resonantly and follow their time evolution in interaction with the hydration shell or excite the OH stretching mode of water and measure the response of AS (PO 2 )- oscillators. Thin films of artificial DNA oligomers containing 23 alternating A-T pairs (Fig. 1a) are cast on 500 nm thick Si 3 N 4 substrates and held in a closed sample cell allowing for a control of
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N H
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Fig. 1 (a) Top: Structure of adenine-thymine (A-T) base pairs in Watson-Crick geometry and sugar and phosphate groups of the DNA backbone. Inset: Scheme of a fully hydrated phosphate group (shaded areas). Bottom: Part of a DNA oligomer containing 23 alternating A-T pairs. (b,d) Transient vibrational spectra of the AS (PO 2 )- mode measured with a spectrally resolved probe detection after resonant excitation for 0% and 92% relative humidity (r.h.). Solid lines: linear infrared absorbance A. (c,e) Time-resolved absorption changes at 0% and 92% r.h. measured at the spectral positions indicated by the arrows in (b,d) (symbols) and calculated kinetics (lines). The residual absorption change found at 0% r.h. is absent for fully hydrated phosphate groups at 92% r.h. Dashed line in (c): Fit curve of the upper transient in (e).
OSA / UP 2010
ME19.pdf
Fig. 2 (a) Linear AS (PO 2 )- absorption of fully hydrated DNA (92% r.h.). (b) Transient AS (PO 2 )- spectra after excitation of the OH stretching mode of the surrounding water shell (symbols, E ex =3500 cm.1). The solid line gives the difference A=A(0%r.h.) –A(92%r.h.) of the linear AS (PO 2 )- absorption at 0% and 92% r.h.
the hydration level [5,6]. The respective pump pulses excite less than 5 percent of the oscillators of DNA and water. The linear AS (PO 2 )- absorption undergoes a red-shift with increasing hydration level. The transient spectra measured after excitation of the AS (PO 2 )- mode (Fig. 1b,d) display an enhanced 1-2 absorption at low frequencies and – at higher frequencies - an absorption decrease on the 0-1 transition that originates from ground state bleaching and stimulated emission from the v=1 state (inset of Fig. 1c). In the transient spectra, spectral diffusion is essentially absent and a lineshape analysis gives vibrational anharmonicities of 122 cm-1 and 182 cm-1 at 0% and 92% relative humidity (r.h.). At the two hydration levels, the time resolved transients in Fig. 1c,e show a fast decay of the absorbance changes with the same time constant of 340 fs, the v=1 lifetime. At 0% r.h. where typically a single water molecule interacts with a phosphate group, the fast relaxation is followed by residual absorbance changes that decay with a time constant of ~6 ps (not shown). The latter signal is absent at 92% r.h. where the phosphate groups are fully hydrated by 6 water molecules each [1,3]. The v=1 population of the AS (PO 2 )- mode decays via DNA modes at lower frequency with a minor role of the hydration shell, resulting in a lifetime independent of the hydration level. At 0%, the excess energy released in the AS (PO 2 )- relaxation heats the excited phosphate groups locally, causing a reshaping of AS (PO 2 )- absorption. This mechanism gives rise to the residual absorption changes in Fig. 1c which decay by picosecond energy transfer within the DNA structure. In the fully hydrated DNA (92% r.h.), the local water shell around an excited phosphate group serves as an efficient heat sink. The absence of any slow signal in Fig. 1e shows that the transfer of excess energy from DNA into water occurs on a femtosecond time scale similar to the v=1 population decay. In Fig. 2, we present transient AS (PO 2 )- spectra for 92% r.h. observed after excitation of the OH stretching mode of the water shell. The spectrum at -200 fs reflects the perturbed free induction decay due to anharmonic coupling of the OH stretching and AS (PO 2 )- modes. The spectra at positive delay times display a drastically different shape with a decrease of absorption at low and an increase at high frequencies. Such changes build up together with a vibrationally hot ground state of the water shell (not shown) and reflect changes in the local pattern of water- phosphate hydrogen bonds. In the hot ground state, water-phosphate bonds are broken and the AS (PO 2 )absorption shifts to higher frequencies. Transient AS (PO 2 )- spectra at long delay times are close to the difference spectrum A of the stationary AS (PO 2 )- absorption for 0% and 92% r.h. (solid line in Fig. 2b) where a reduced hydration level results in a smaller number of water molecules and, thus, water-phosphate hydrogen bonds. In summary, our results establish a detailed microscopic picture of DNA-water interactions. References [1] [2] [3] [4] [5] [6]
B. Schneider, K. Patel, H. M. Berman, "Hydration of the phosphate group in double-helical DNA", Biophys. J. 75, 2422-2434 (1998). N. Korolev, A. P. Lyubartsev, A. Laaksonen, L. Nordenskiöld, "On the competition between water, sodium ions, and spermine in binding to DNA: A molecular dynamics computer simulation study", Biophys. J. 82, 2860-2875 (2002). Ł. Szyc, M. Yang, E. T. J. Nibbering, T. Elsaesser, "Ultrafast vibrational dynamics and local interactions of hydrated DNA", Angew. Chem. Int. Ed., in press (2010). Ł. Szyc, M. Yang, T. Elsaesser, "Ultrafast energy exchange via phosphate-water interactions in hydrated DNA", J. Phys. Chem. B, submitted. J. R. Dwyer, Ł. Szyc, E. T. J. Nibbering, T. Elsaesser, "Ultrafast vibrational dynamics of adenine-thymine base pairs in DNA oligomers", J. Phys. Chem. B 112, 11194-11197 (2008). Ł. Szyc, J. R. Dwyer, E. T. J. Nibbering, T. Elsaesser, "Ultrafast dynamics of N-H and O-H stretching excitations in hydrated DNA oligomers", Chem. Phys. 357, 36-44 (2009).
