Chromophore/DNA Interactions: Femto- to Nanosecond Spectroscopy, NMR Structure, and Electron Transfer Theory
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- 作者：Till von Feilitzsch ; Jennifer Tuma ; Heike Neubauer ; Laurent Verdier ; Reinhard Haselsberger ; Reiner Feick ; Gagik Gurzadyan ; Alexander A. Voityuk ; Christian Griesinger ; Maria E. Michel-Beyerle
- 刊名：Journal of Physical Chemistry B
- 出版年：2008
- 出版时间：January 24, 2008
- 年：2008
- 卷：112
- 期：3
- 页码：973 - 989
- 全文大小：579K
- 年卷期：v.112,no.3(January 24, 2008)
- ISSN：1520-5207
文摘
The mechanism of photoinduced hole injection into DNA has been studied using an integrated approach thatcombines NMR structural analysis, time-resolved spectroscopy, and quantum-chemical calculations. Acovalently linked acridinium derivative, the protonated 9-amino-6-chloro-2-methoxyacridine (X+), is replacinga thymine and separated from either guanine (G) or the easier to oxidize 7-deazaguanine (Z) by one adenine·thymine (A·T) base pair. The key features of this donor/acceptor system are the following: (i) In more than95% of the duplexes, X+ is located in a central, coplanar position between the neighboring A·T base pairswith its long axis in parallel showing minimal twist and tilt angles (<15
). The complementary adenine baseis turned out into the extrahelical space. In a minority of less than 5%, X+ is found to be still attached to theduplex. X+ is most probably associated with one of the phosphates, since it is neither intercalated betweenmore remote base pairs nor bound to sugars or grooves. This minority characterized by an excited statelifetime >10 ns gives rise to a small background signal in time-resolved measurements and contributespredominantly to steady-state fluorescence spectra. (ii) Although the intercalation mode of X+ is well defined,the NMR structure reveals that there are two conformations of X+ with respect to the arrangement of itsmethoxy substituent. In one conformation, the methoxy group is in the plane of the chromophore, while, inthe other extraplanar conformation, the methoxy group forms an angle of 70 with the acridinium ring. Thefluorescence decay of 5'-ZAX and 5'-GAX tracts can be fitted to a biexponential function with similaramplitudes, reflecting the oxidation dynamics of G and Z, with the slower rate being determined by largerthermal activation energy. The attribution of biexponential electron transfer (ET) dynamics to the bimodalorientation of the methoxy group at the acridinium is supported by quantum-chemical calculations. Thesepredict a larger free energy change for hole transfer in the nonplanar conformation as compared to the planarone, whereas the difference in the electronic couplings is negligible. (iii) Kinetic studies of the directionalityof the 1(X+)* induced hole injection reveal similarly fast decay components in both directions of the duplex,that is, in 5'-ZAX and 5'-XAZ, with the amplitude of the fast component being significantly reduced in5'-XAZ. The NMR structure shows that local structural deviations from B-DNA are much more pronouncedin the 3'-5' direction than in the 5'-3' direction. According to quantum-chemical calculations, the directionalityof charge injection is not a universal feature of the DNA duplex but depends critically on the rotation angleof the aromatic plane of the acridinium within the 
stack. The arrangement of X+ in 5'-ZAX and 5'-XAZcorresponds to a conformation with weak directionality of the electronic couplings. The increased disorder inthe 3'-5'direction favors slow hole transfer components at the expense of the fast ones. (iv) A comparison ofthe hole transfer in 5'-GAX and 5'-ZAG shows that classical Marcus theory can explain the ratio of thecharge shift rates of more than 2 orders of magnitude on the basis of a free energy difference between G andZ of 0.3 eV. Both NMR structures and quantum-chemical calculations justify the appreciable neglect ofdifferences of electronic couplings as well as in the reorganization energy in 5'-GAX and 5'-ZAG. Despitethe attractive concept for the behavior of floppy DNA oligonucleotides, in this acridinium/DNA system,there is no evidence for conformational gating, that is, for fluctuations in the electronic couplings that permitthe ET to occur.
). The complementary adenine baseis turned out into the extrahelical space. In a minority of less than 5%, X+ is found to be still attached to theduplex. X+ is most probably associated with one of the phosphates, since it is neither intercalated betweenmore remote base pairs nor bound to sugars or grooves. This minority characterized by an excited statelifetime >10 ns gives rise to a small background signal in time-resolved measurements and contributespredominantly to steady-state fluorescence spectra. (ii) Although the intercalation mode of X+ is well defined,the NMR structure reveals that there are two conformations of X+ with respect to the arrangement of itsmethoxy substituent. In one conformation, the methoxy group is in the plane of the chromophore, while, inthe other extraplanar conformation, the methoxy group forms an angle of 70 with the acridinium ring. Thefluorescence decay of 5'-ZAX and 5'-GAX tracts can be fitted to a biexponential function with similaramplitudes, reflecting the oxidation dynamics of G and Z, with the slower rate being determined by largerthermal activation energy. The attribution of biexponential electron transfer (ET) dynamics to the bimodalorientation of the methoxy group at the acridinium is supported by quantum-chemical calculations. Thesepredict a larger free energy change for hole transfer in the nonplanar conformation as compared to the planarone, whereas the difference in the electronic couplings is negligible. (iii) Kinetic studies of the directionalityof the 1(X+)* induced hole injection reveal similarly fast decay components in both directions of the duplex,that is, in 5'-ZAX and 5'-XAZ, with the amplitude of the fast component being significantly reduced in5'-XAZ. The NMR structure shows that local structural deviations from B-DNA are much more pronouncedin the 3'-5' direction than in the 5'-3' direction. According to quantum-chemical calculations, the directionalityof charge injection is not a universal feature of the DNA duplex but depends critically on the rotation angleof the aromatic plane of the acridinium within the stack. The arrangement of X+ in 5'-ZAX and 5'-XAZcorresponds to a conformation with weak directionality of the electronic couplings. The increased disorder inthe 3'-5'direction favors slow hole transfer components at the expense of the fast ones. (iv) A comparison ofthe hole transfer in 5'-GAX and 5'-ZAG shows that classical Marcus theory can explain the ratio of thecharge shift rates of more than 2 orders of magnitude on the basis of a free energy difference between G andZ of 0.3 eV. Both NMR structures and quantum-chemical calculations justify the appreciable neglect ofdifferences of electronic couplings as well as in the reorganization energy in 5'-GAX and 5'-ZAG. Despitethe attractive concept for the behavior of floppy DNA oligonucleotides, in this acridinium/DNA system,there is no evidence for conformational gating, that is, for fluctuations in the electronic couplings that permitthe ET to occur.