The effect of varied ion distributions on long-range DNA charge transport

Helix-Dependent Spin Filtering through the DNA Duplex

Recent work suggests that electrons can travel through DNA and other chiral molecules in a spin-selective manner, but little is known about the origin of this spin selectivity. Here we describe experiments on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. Our results show that the two spins migrate through duplex DNA with a different yield and that spin selectivity requires charge transport through the DNA duplex. Significantly, shifting the same duplex DNA between right-handed B- and left-handed Z-forms leads to a diode-like switch in spin selectivity; which spin moves more efficiently through the duplex depends upon the DNA helicity. With DNA, the supramolecular organization of chiral moieties, rather than the chirality of the individual monomers, determines the selectivity in spin, and thus a conformational change can switch the spin selectivity.

Electrical characterization of DNA supported on nitrocellulose membranes

Integrated DNA-based nanoscale electronic devices will enable the continued realization of Moore’s Law at the level of functional devices and systems. In this work, the electrical characterization of single and complementary base paired DNA has been directly measured and investigated via the use of nitrocellulose membranes. A radio frequency DAKS-3.5 was used to measure the reflection coefficients of different DNA solutions dotted onto nitrocellulose membranes. Each DNA solution was exposed to a radio frequency signal with a power of 10 dBm and with a sweep from 200 MHz up to 13.6 GHz. The conducted measurements show some distinctions between the homomeric and complementary bases due to their different electrical polarization. As revealed from the measurements conducted, with the addition of DNA oligonucleotides, the measured capacitance increased when compared with buffer medium alone. The DNA molecules could be modeled as dielectric material that can hold electrical charges. Furthermore, the complementary paired DNA molecule-based inks solutions had a higher capacitance value compared with single DNA molecules (A, C, G and T) solutions.

Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics

In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.

Long-range radical cation migration in DNA: Investigation of the mechanism

During the past decade, long-range radical cation migration in DNA has been an area of extensive experimental and theoretical examination. The motivations for the vigorous investigation of this topic are its potential to yield a deeper understanding of the processes that cause oxidative damage of genomic DNA and the potential for use of DNA architectures in molecular electronics. This investigation has revealed the mechanisms of charge transport and the limitations of DNA as a functional element in devices. In this article we discuss various aspects of the radical cation migration process and present the plausible mechanism by which this process occurs.

Design Aspects for the Development of Mixed-Metal Supramolecular Complexes Capable of Visible Light Induced Photocleavage of DNA

Mixed-metal supramolecular complexes that couple ruthenium or osmium based light absorbers to a central rhodium(III) core have been designed which photocleave DNA upon irradiation with visible light. The complexes [[(bpy)(2)Ru(dpp)](2)RhCl(2)](PF(6))(5), [[(bpy)(2)Os(dpp)](2)RhCl(2)](PF(6))(5), and [[(tpy)RuCl(dpp)](2)RhCl(2)](PF(6))(3), where bpy = 2,2'-bipyridine, tpy = 2,2':6',2' '-terpyridine, and dpp = 2,3-bis(2-pyridyl)pyrazine, all exhibit intense metal to ligand charge transfer (MLCT) based transitions in the visible but possess lower lying metal to metal charge transfer (MMCT) excited states. These supramolecular complexes with low lying MMCT states photocleave DNA when excited into their intense MLCT transitions. Structurally similar complexes without this low lying MMCT state do not exhibit DNA photocleavage, establishing the role of this MMCT state in the DNA photocleavage event. Design considerations necessary to produce functional DNA photocleavage agents are presented herein.

Pathways for Photoinduced Charge Separation in DNA Hairpins

By means of correlated quantum-chemical calculations, we explore the chain-length dependence of the electronic coupling for photoinduced charge separation in DNA hairpins associated to conjugated linkers. Pathways for charge transfer from the linker chromophore to a guanine site located at a well-defined distance along the DNA strand are identified. Importantly, these involve not only the frontier molecular orbitals of the interacting donor, bridge, and acceptor units, but also deeper lying orbitals possessing both the appropriate energy and the symmetry to overlap significantly. The relative efficiency of these channels is found to be sensitive to the chemical structure of the linker, leading to falloff parameters for the charge-transfer rates ranging from approximately 0.4 to approximately 1.2 A(-1).

Synthesis, characterization, DNA-binding and cleavage studies of [Ru(bpy)2(actatp)]2+ and [Ru(phen)2(actatp)]2+ (actatp=acenaphthereno[1,2-b]-1,4,8,9-tetraazariphenylence)

New ligand acenaphthereno[1,2-b]-1,4,8,9-tetraazariphenylence (actatp) and its complexes [Ru(bpy)(2)(actatp)](ClO(4))(2).2H(2)O (1) (bpy=2,2'-bipyridine) and [Ru(phen)(2)(actatp)](ClO(4))(2).2H(2)O (2) (phen=1,10-phenanthroline) have been synthesized and characterized by UV-vis, 1H NMR, and mass spectra. The electrochemical behavior of the two complexes was studied by cyclic voltammetry. The interaction of the two complexes with calf thymus DNA has been investigated by spectrophotometric methods and viscosity measurements. The experimental results suggest that both complexes bind to DNA through an intercalative mode. The circular dichroism signals of the dialysates of the racemic complexes against calf thymus DNA are discussed. When irradiated at 302 nm, both complexes have also been found to promote the photocleavage of plasmid pBR 322 DNA.

DNA-protein cross-linking via guanine oxidation: dependence upon protein and photosensitizer

DNA-protein cross-links form when guanine undergoes a 1-electron oxidation in a flash-quench experiment, and the importance of reactive oxygen species, protein, and photosensitizer is examined here. In these experiments, a strong oxidant produced by oxidative quenching of a DNA-bound photosensitizer generates an oxidized guanine base that reacts with protein to form the covalent adduct. These cross-links are cleaved by hot piperidine and are not the result of reactive oxygen species, since neither a hydroxyl radical scavenger (mannitol) nor oxygen affects the yield of DNA-histone cross-linking, as determined via a chloroform extraction assay. The cross-linking yield depends on protein, decreasing as histone > cytochrome c > bovine serum albumin. The yield does not depend on the cytochrome oxidation state, suggesting that reduction of the guanine radical by ferrocytochrome c does not compete effectively with cross-linking. The photosensitizer strongly influences the cross-linking yield, which decreases in the order Ru(phen)(2)dppz(2+) [phen = 1,10-phenanthroline; dppz = dipyridophenazine] > Ru(bpy)(3)(2+) [bpy = 2,2'-bipyridine] > acridine orange > ethidium, in accordance with measured oxidation potentials. A long-lived transient absorption signal for ethidium dication in poly(dG-dC) confirms that guanine oxidation is inefficient for this photosensitizer. From a polyacrylamide sequencing gel of a (32)P-labeled 40-mer, all of these photosensitizers are shown to damage guanines preferentially at the 5' G of 5'-GG-3' steps, consistent with a 1-electron oxidation. Additional examination of ethidium shows that it can generate cross-links between histone and plasmid DNA (pUC19) and that the yield depends on the quencher. Altogether, these results illustrate the versatility of the flash-quench technique as a way to generate physiologically relevant DNA-protein adducts via the oxidation of guanine and expand the scope of such cross-linking reactions to include proteins that may associate only transiently with DNA.

Long-range DNA charge transport

The stack of base pairs within double helical DNA has been shown to mediate charge transport reactions. Charge transport through DNA can result in chemistry at a distance, yielding oxidative DNA damage at a site remote from the bound oxidant. Since DNA charge transport chemistry depends on coupling within the stacked base pair array, this chemistry is remarkably sensitive to sequence-dependent DNA structure and dynamics. Here, we discuss different features of DNA charge transport chemistry, including applications as well as possible biological consequences and opportunities.

Visible light induced photocleavage of DNA by a mixed-metal supramolecular complex: [[(bpy)(2)Ru(dpp)](2)RhCl2]5+

The mixed-metal supramolecular complex, [[(bpy)(2)Ru(dpp)](2)RhCl(2)](PF(6))(5) (bpy = 2,2'-bipyridine and dpp = 2,3-bis(2-pyridyl)pyrazine) coupling two ruthenium light absorbers (LAs) to a central rhodium, has been shown to photocleave DNA. This system possesses a lowest lying metal to metal charge transfer (MMCT) excited state in contrast to the metal to ligand charge transfer states (MLCT) of the bpm and Ir analogues. The systems with an MLCT excited state do not photocleavage DNA. [[(bpy)(2)Ru(dpp)](2)RhCl(2)](PF(6))(5) is the first supramolecular system shown to cleave DNA. It functions through an excited state previously unexplored for this reactivity, a Ru --> Rh MMCT excited state. This system functions when irradiated with low energy visible light with or without molecular oxygen.

Charge transport in DNA

The base pair stack within double helical DNA provides an effective medium for charge transport. The DNA pi-stack mediates oxidative DNA damage over long molecular distances in a reaction that is exquisitely sensitive to the sequence-dependent conformation and dynamics of DNA. A mixture of tunneling and hopping mechanisms have been proposed to account for this long-range chemistry, which is gated by dynamical variations within the stack. Electrochemical sensors have also been developed, based upon the sensitivity of DNA charge transport to base pair stacking, and these sensors provide a completely new approach to diagnosing single base mismatches in DNA and monitoring protein-DNA interactions electrically. DNA charge transport, furthermore, may play a role within the cell and, indeed, oxidative damage to DNA from a distance has been demonstrated in the cell nucleus. As a result, the biological consequences of and opportunities for DNA-mediated charge transport now require consideration.