Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates

Abstract

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...

Conformational Switching of Pyrenes Associated on Hairpin Loop Region by DNA B‐Z Transition

“…[20][21][22] DNA and its analogues can be used as templates to construct helical chromophore associates through π-interactions in a precise manner. [23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] Helical chromophore associates have unique properties that differ significantly from those of the monomeric state. The manner in which chromophores associate depends on the structure of the DNA-template.…”

“…DNA and its analogues can be used as templates to construct helical chromophore associates through π‐interactions in a precise manner [23–38] . Helical chromophore associates have unique properties that differ significantly from those of the monomeric state.…”

Enzymatic synthesis of biphenyl-DNA oligonucleotides

“…[34] Interestingly, up to 7 consecutive biphenyl base pairs can be incorporated into DNA without causing any decrease in duplex stability [32] and an NMR investigation concluded that stacking interactions were the main driving force behind the impressive stability of these UBPs. [35] The zipper-like motif thus appears to be an alluring candidate for applications such as electron transport through nucleic acids [36][37][38] or an expansion of the genetic code. [39] Besides biphenylmodified DNA, other C-nucleosides equipped with aromatic residues play central roles in numerous applications including the induction of important conformational transitions, [40] relaying electron transport through duplexes, [37,38,[41][42][43] assisting the homogenous assembly of aromatic carbon layers, [44] or labeling of oligonucleotides with fluorophores.…”

Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions

“…The B‐ to Z‐DNA transition, which plays a crucial role in biological systems, has been utilized for nanomechanical devices and nanosensors . In addition, DNA and DNA analogues have been used as templates to construct helical chromophore associations with π interactions through the precise incorporation of multiple chromophores into DNA . Such helical chromophore associations demonstrate unique properties, which differ significantly from the monomeric state.…”