Experimental section GeneralAll reactions were performed under argon in oven-dried glassware. Anhydrous solvents were obtained by filtration through activated aluminum oxide. Unless stated otherwise all chemicals and solvents were purchased from Sigma. Solvents for extractions and flash chromatography were distilled before use. Flash column chromatography (FCC) was performed using silica gel (230-400 mesh) from Silicycle. Thin layer chromatography was carried out on glass-backed plates precoated with silica gel (0.25mm, UV 254 ) from Macherey-Nagel. 1 H NMR was recorded at 300MHz or 400MHz on a Bruker AC-300 or a Bruker DRX-400. 13 C NMR (75 MHz) was recorded on a Bruker AC-300. 31 P NMR spectra were recorded at 121.4 MHz using 85% H 3 PO 4 as an external standard. All spectra were referenced to the signals of the corresponding solvent. Chemical shifts are given in ppm (δ scale) and coupling constants (J) in Hz. High resolution electrospray ionization (ESI) mass spectra were recorded on a Thermo Scientific LTQ Orbitrap XL instrument. HPLC purification was performed using an Äkta™ basic 10/100 system (Amersham Pharmacia Biotech) equipped with a Phenomenex Jupiter semi-preparative RP-HPLC column (5μm, C18, 300Å).

DNA duplexes containing unnatural base-pair surrogates are attractive biomolecular nanomaterials with potentially beneficial photophysical or electronic properties. Herein we report the first X-ray structure of a duplex containing a phen-pair in the center of the double helix in a zipper like stacking arrangement.

The modulation of excess electron transfer (EET) within DNA containing a dimethylaminopyrene (C-AP) as an electron donor and 5-bromouracil ( Br dU) as a electron acceptor through phenanthrenyl pairs (phen-R) could be achieved by modifying the phenanthrenyl base surrogates with electron withdrawing and donating groups. Arranging the phenanthrenyl units to form a descending LUMO gradient increased the EET efficiency compared to the electron transfer through uniform LUMOs or an ascending LUMO gradient.The well-defined double helical structure of DNA with the linear arranged base pairs represents a suitable scaffold for charge transfer and is therefore subject to intense studies in DNA damage, [1] sensors [2] and applications in molecular electronics.[3]The reductive electron transfer also called excess electron transfer (EET) in DNA is a process that is directed through the lowest unoccupied molecular orbital (LUMO) of the DNA bases. Investigations elucidated that the charge transfer over longer distances occurs via electron hopping mostly through thymine bases (k = 10 10 s -1). [4] In earlier studies it was shown that the replacement of the natural base pairs by non-hydrogen bonding base surrogates with extended aromatic surfaces such as phenanthrene could have beneficial conducting properties and could overcome the physico-chemical limitations of the natural nucleobases.[5] Regarding the reduction of such base surrogates the choice of the electron injector is crucial for the success of the experiments. Investigations by Grigorenko et. al. revealed that pyrene ( Py dU, Ered* = -2.2 V vs NHE) [6] only enables a superexchange mechanism, whereas phenothiazine (PTZ, Ered* = -2.7 V vs SCE) [7] allowed to trigger the system into an electron hopping mechanism with a transport that spreads over longer distances.[5] A photoexcitable dimethyl amino-pyrenyl donor attached to a deoxyuracil ( AP dU, Ered* = -2.2 V vs NHE) [8] that exhibits suitable redox properties for long range charge transfer experiments was successfully used by Bätzner et. al. to inject an electron in hydroquinoline base surrogates. [9] In this study, we investigated the EET through DNA containing phenanthrenyl base surrogates with different reduction potentials and LUMO energy levels. It is believed that the electron transfer within DNA can be modulated by the installation of a potential energy gradient.[10] The predicted advantage of such a redox/LUMO gradient was envisioned to be the unidirectionality of the electron transfer and therefore a gain in efficiency. The installation of the different reduction potentials was deemed to be possible by the introduction of electron withdrawing (CN) and donating (NH2) groups at the 7-position of the phenanthrene (phen). The synthesis of the NH2 phen and phen phosphoramidites applicable for automated DNA synthesis was performed according to published procedures.[11] The introduction of a cyano group required a palladium catalyzed substitution of the intermediate 9 with copper-(I)-cyanide. Tritiylation and phosphiti...

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