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Base stacking controls excited-state dynamics in A·T DNA


Solar ultraviolet light creates excited electronic states in DNA that can decay to mutagenic photoproducts. This vulnerability is compensated for in all organisms by enzymatic repair of photodamaged DNA. As repair is energetically costly, DNA is intrinsically photostable. Single bases eliminate electronic energy non-radiatively on a subpicosecond timescale1, but base stacking and base pairing mediate the decay of excess electronic energy in the double helix in poorly understood ways. In the past, considerable attention has been paid to excited base pairs2. Recent reports have suggested that light-triggered motion of a proton in one of the hydrogen bonds of an isolated base pair initiates non-radiative decay to the electronic ground state3,4. Here we show that vertical base stacking, and not base pairing, determines the fate of excited singlet electronic states in single- and double-stranded oligonucleotides composed of adenine (A) and thymine (T) bases. Intrastrand excimer states with lifetimes of 50–150 ps are formed in high yields whenever A is stacked with itself or with T. Excimers limit excitation energy to one strand at a time in the B-form double helix, enabling repair using the undamaged strand as a template.

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Figure 1: DNA photophysical pathways as a function of base pairing and base stacking interactions.
Figure 2: Femtosecond pump–probe transients for the single-stranded oligonucleotide (dA) 18 (filled circles) and the 5′-mononucleotide AMP (open circles).
Figure 3: Transient absorption versus time at several probe wavelengths for the single-stranded oligonucleotide d(T) 18 (filled circles) and its constituent 5′-mononucleotide, TMP (open circles).
Figure 4: Singlet excited-state dynamics in double-stranded oligonucleotides. a, Transient absorption at indicated probe wavelengths (top, 570 nm; bottom, 250 nm) following 266 nm excitation of (dA)18·(dT)18 (triangles).


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This work was supported by the NIH and performed using laser instrumentation in Ohio State's Center for Chemical and Biophysical Dynamics funded by the NSF. B.K. acknowledges support from the Alexander von Humboldt Foundation.

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Correspondence to Bern Kohler.

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Supplementary information

Supplementary Figures S1–S4

These 4 figures show the kinetic data from Figures 2 through 4 on conventional, linear time axes. (DOC 160 kb)

Supplementary Figure S5

This figure depicts the steady-state UV absorption spectra of the investigated compounds before and after 30 min of irradiation at the excitation pump wavelength of 266 nm. (DOC 42 kb)

Supplementary Figure S6

This figure shows the UV-melting profiles for the double-stranded oligonucleotides at 260 nm. This confirms that both (dA)18·(dT)18, and the alternating oligonucleotide, d(AT)9·d(AT)9 are double stranded at room temperature. (DOC 31 kb)

Supplementary Figure S7

This figure shows the room-temperature circular dichroism spectra for the double-stranded oligonucleotides. (DOC 28 kb)

Supplementary Tables S1–S4

These tables list the parameters obtained by global fitting to the kinetic traces presented in Figures 1 through 4 and Supplementary Figures 1 through 4. (DOC 74 kb)

Supplementary Discussion

This file contains discussion regarding the two photon absorption signal seen in the UV probe measurements. (DOC 20 kb)

Supplementary Methods

This file contains the methods used to measure circular dichroism spectra and melting profiles. (DOC 19 kb)

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Crespo-Hernández, C., Cohen, B. & Kohler, B. Base stacking controls excited-state dynamics in A·T DNA. Nature 436, 1141–1144 (2005).

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