DNA Molecular Photonics¶†

Excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate

Minor structural modifications to the DNA and RNA nucleobases have a significant effect on their excited state dynamics and electronic relaxation pathways. In this study, the excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate are investigated in aqueous solution and in a mixture of methanol and water using femtosecond broadband transient absorption spectroscopy following excitation at 267 nm. The transient spectra are collected using photon densities that ensure no parasitic multiphoton-induced signal from solvated electrons. The data can be fit satisfactorily using a two- or three-component kinetic model. By analyzing the results from steady-state, time-resolved, computational calculations, and the methanol-water mixture, the following general relaxation mechanism is proposed for both molecules, L_b → L_a → ¹πσ^*(ICT) → S₀, where the ¹πσ^*(ICT) stands for an intramolecular charge transfer excited singlet state with significant πσ^* character. In general, longer lifetimes for internal conversion are obtained for 7-deazaguanosine compared to guanosine 5'-monophosphate. Internal conversion of the ¹πσ^*(ICT) state to the ground state occurs on a similar time scale of a few picoseconds in both molecules. Collectively, the results demonstrate that substitution of a single nitrogen atom for a methine (C-H) group at position seven of the guanine moiety stabilizes the ¹ππ^* L_b and L_a states and alters the topology of their potential energy surfaces in such a way that the relaxation dynamics in 7-deazaguanosine are slowed down compared to those in guanosine 5'-monophosphate but not for the internal conversion of ¹πσ^*(ICT) state to the ground state.

Electromagnetic and optical characteristics of Nb5+-doped double-crossover and salmon DNA thin films

We report the fabrication and physical characteristics of niobium ion (Nb⁵⁺)-doped double-crossover DNA (DX-DNA) and salmon DNA (SDNA) thin films. Different concentrations of Nb⁵⁺ ([Nb⁵⁺]) are coordinated into the DNA molecules, and the thin films are fabricated via substrate-assisted growth (DX-DNA) and drop-casting (SDNA) on oxygen plasma treated substrates. We conducted atomic force microscopy to estimate the optimum concentration of Nb⁵⁺ ([Nb⁵⁺]_O = 0.08 mM) in Nb⁵⁺-doped DX-DNA thin films, up to which the DX-DNA lattices maintain their structures without deformation. X-ray photoelectron spectroscopy (XPS) was performed to probe the chemical nature of the intercalated Nb⁵⁺ in the SDNA thin films. The change in peak intensities and the shift in binding energy were witnessed in XPS spectra to explicate the binding and charge transfer mechanisms between Nb⁵⁺ and SDNA molecules. UV-visible, Raman, and photoluminescence (PL) spectra were measured to determine the optical properties and thus investigate the binding modes, Nb⁵⁺ coordination sites in Nb⁵⁺-doped SDNA thin films, and energy transfer mechanisms, respectively. As [Nb⁵⁺] increases, the absorbance peak intensities monotonically increase until ∼[Nb⁵⁺]_O and then decrease. However, from the Raman measurements, the peak intensities gradually decrease with an increase in [Nb⁵⁺] to reveal the binding mechanism and binding sites of metal ions in the SDNA molecules. From the PL, we observe the emission intensities to reduce them at up to ∼[Nb⁵⁺]_O and then increase after that, expecting the energy transfer between the Nb⁵⁺ and SDNA molecules. The current-voltage measurement shows a significant increase in the current observed as [Nb⁵⁺] increases in the SDNA thin films when compared to that of pristine SDNA thin films. Finally, we investigate the temperature dependent magnetization in which the Nb⁵⁺-doped SDNA thin films reveal weak ferromagnetism due to the existence of tiny magnetic dipoles in the Nb⁵⁺-doped SDNA complex.

Ultrafast Response in AC-Driven Electrochemiluminescent Cell Using Electrochemically Active DNA/Ru(bpy)32+ Hybrid Film with Mesoscopic Structures

Electrochemiluminescence (ECL) refers to light emission induced by an electrochemical redox reaction. The stability, emission response, and light intensity of the ECL device are known to be improved by using an alternating current (AC) voltage. In this paper, an AC-driven ECL device is fabricated with DNA/Ru(bpy)₃²⁺ hybrid film-modified electrode. The Ru(bpy)₃²⁺ complex exhibits significant electrochemical reactivity in the DNA/Ru(bpy)₃²⁺ hybrid film prepared by electrochemical adsorption. The hybrid film contains unique micrometre-scale aggregates of Ru(bpy)₃²⁺ in DNA matrix. The physicochemical properties of the hybrid film and its AC-driven ECL characteristics in the electrochemical device are studied. Orange-coloured ECL is observed to be emitted from only the aggregated structures in the hybrid film at the high AC frequency of 10 kHz, which corresponds to a response time shorter than 100 μs.

Ultra-low Doping on Two-Dimensional Transition Metal Dichalcogenides using DNA Nanostructure Doped by a Combination of Lanthanide and Metal Ions

Here, we propose a novel DNA-based doping method on MoS₂ and WSe₂ films, which enables ultra-low n- and p-doping control and allows for proper adjustments in device performance. This is achieved by selecting and/or combining different types of divalent metal and trivalent lanthanide (Ln) ions on DNA nanostructures, using the newly proposed concept of Co-DNA (DNA functionalized by both divalent metal and trivalent Ln ions). The available n-doping range on the MoS₂ by Ln-DNA is between 6 × 10⁹ and 2.6 × 10¹⁰cm⁻². The p-doping change on WSe₂ by Ln-DNA is adjusted between −1.0 × 10¹⁰ and −2.4 × 10¹⁰cm⁻². In Eu³⁺ or Gd³⁺-Co-DNA doping, a light p-doping is observed on MoS₂ and WSe₂ (~10¹⁰cm⁻²). However, in the devices doped by Tb³⁺ or Er³⁺-Co-DNA, a light n-doping (~10¹⁰cm⁻²) occurs. A significant increase in on-current is also observed on the MoS₂ and WSe₂ devices, which are, respectively, doped by Tb³⁺- and Gd³⁺-Co-DNA, due to the reduction of effective barrier heights by the doping. In terms of optoelectronic device performance, the Tb³⁺ or Er³⁺-Co-DNA (n-doping) and the Eu³⁺ or Gd³⁺-Co-DNA (p-doping) improve the MoS₂ and WSe₂ photodetectors, respectively. We also show an excellent absorbing property by Tb³⁺ ions on the TMD photodetectors.

Construction and characterization of Cu²⁺, Ni²⁺, Zn²⁺, and Co²⁺ modified-DNA crystals

We studied the physical characteristics of modified-DNA (M-DNA) double crossover crystals fabricated via substrate-assisted growth with various concentrations of four different divalent metallic ions, Cu(2+), Ni(2+), Zn(2+), and Co(2+). Atomic force microscopy (AFM) was used to test the stability of the M-DNA crystals with different metal ion concentrations. The AFM images show that M-DNA crystals formed without deformation at up to the critical concentrations of 6 mM of [Cu(2+)], 1.5 mM of [Ni(2+)], 1 mM of [Zn(2+)], and 1 mM of [Co(2+)]. Above these critical concentrations, the M-DNA crystals exhibited deformed, amorphous structures. Raman spectroscopy was then used to identify the preference of the metal ion coordinate sites. The intensities of the Raman bands gradually decreased as the concentration of the metal ions increased, and when the metal ion concentrations increased beyond the critical values, the Raman band of the amorphous M-DNA was significantly suppressed. The metal ions had a preferential binding order in the DNA molecules with G-C and A-T base pairs followed by the phosphate backbone. A two-probe station was used to measure the electrical current-voltage properties of the crystals which indicated that the maximum currents of the M-DNA complexes could be achieved at around the critical concentration of each ion. We expect that the functionalized ion-doped M-DNA crystals will allow for efficient devices and sensors to be fabricated in the near future.

Photoinduced electron transfer between 2-methylanthraquinone and triethylamine in an ionic liquid: time-resolved EPR and transient absorption spectroscopy study

Photoinduced electron transfer between 2-methylanthraquinone (MeAQ) and triethylamine (TEA) in a room-temperature ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]), was investigated by comparing the time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy and the transient absorption spectroscopy. The results of TR-EPR spectroscopy, in which MeAQ was 8 mmol L(-1) and TEA was 150 mmol L(-1), indicated that the transient radical would exist longer time in [bmim][PF6] than in acetonitrile. At the delay time of 8 μs after laser excitation, the TR-EPR signal transformed from an emissive peak into an absorptive peak when the experiment was performed in [bmim][PF6]. The results of the transient absorption spectroscopy, in which MeAQ was 0.1 mmol L(-1) and TEA was 2.2 mmol L(-1), showed that the efficiency and the rate of the photoinduced electron transfer reaction in [bmim][PF6] were obviously lower than that in acetonitrile. It was concluded that various factors, such as concentration, viscosity and local structural transformation of the solution, have an influence on the process of photoinduced electron transfer in [bmim][PF6].

n- and p-Type doping phenomenon by artificial DNA and M-DNA on two-dimensional transition metal dichalcogenides

Deoxyribonucleic acid (DNA) and two-dimensional (2D) transition metal dichalcogenide (TMD) nanotechnology holds great potential for the development of extremely small devices with increasingly complex functionality. However, most current research related to DNA is limited to crystal growth and synthesis. In addition, since controllable doping methods like ion implantation can cause fatal crystal damage to 2D TMD materials, it is very hard to achieve a low-level doping concentration (nondegenerate regime) on TMD in the present state of technology. Here, we report a nondegenerate doping phenomenon for TMD materials (MoS2 and WSe2, which represent n- and p-channel materials, respectively) using DNA and slightly modified DNA by metal ions (Zn(2+), Ni(2+), Co(2+), and Cu(2+)), named as M-DNA. This study is an example of interdisciplinary convergence research between DNA nanotechnology and TMD-based 2D device technology. The phosphate backbone (PO4(-)) in DNA attracts and holds hole carriers in the TMD region, n-doping the TMD films. Conversely, M-DNA nanostructures, which are functionalized by intercalating metal ions, have positive dipole moments and consequently reduce the electron carrier density of TMD materials, resulting in p-doping phenomenon. N-doping by DNA occurs at ∼6.4 × 10(10) cm(-2) on MoS2 and ∼7.3 × 10(9) cm(-2) on WSe2, which is uniform across the TMD area. p-Doping which is uniformly achieved by M-DNA occurs between 2.3 × 10(10) and 5.5 × 10(10) cm(-2) on MoS2 and between 2.4 × 10(10) and 5.0 × 10(10) cm(-2) on WSe2. These doping levels are in the nondegenerate regime, allowing for the proper design of performance parameters of TMD-based electronic and optoelectronic devices (VTH, on-/off-currents, field-effect mobility, photoresponsivity, and detectivity). In addition, by controlling the metal ions used, the p-doping level of TMD materials, which also influences their performance parameters, can be controlled. This interdisciplinary convergence research will allow for the successful integration of future layered semiconductor devices requiring extremely small and very complicated structures.

Magnetic characteristics of copper ion-modified DNA thin films

We developed a new method of fabricating a divalent copper ion (Cu²⁺) modified DNA thin film on a glass substrate and studied its magnetic properties. We evaluated the coercive field (H_c), remanent magnetization (M_r), susceptibility (χ), and thermal variation of magnetization with varying Cu²⁺ concentrations [Cu²⁺] resulting in DNA thin films. Although thickness of the two dimensional DNA thin film with Cu²⁺ in dry state was extremely thin (0.6 nm), significant ferromagnetic signals were observed at room temperature. The DNA thin films with a [Cu²⁺] near 5 mM showed the distinct S-shape hysteresis with appreciable high H_c, M_r and χ at low field (≤600 Oe). These were primarily caused by the presence of small magnetic dipoles of Cu²⁺ coordination on the DNA molecule, through unpaired d electrons interacting with their nearest neighbors and the inter-exchange energy in the magnetic dipoles making other neighboring dipoles oriented in the same direction.

In situ generated AgBr-enhanced ZnO nanorod-based photoelectrochemical aptasensing via layer-by-layer assembly

A robust aptasensor for Ag(+) was proposed for the first time using an enhanced ZnO nanorod-based photoelectrochemistry by in situ generated AgBr via layer-by-layer assembly. This work opens up new avenues for application of one-dimensional ZnO nanorod arrays in photoelectrochemical sensing. Additionally, the strategy of employing in situ generated narrow-bandgap semiconductors paves a new way for photoelectrochemical sensing.

Study of picosecond processes of an intercalated dipyridophenazine Cr(iii) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods

Excited-state quenching of DNA intercalated [Cr(phen)₂(dppz)]³⁺ by guanine proceeds by rapid forward and back electron transfer of <3 ps.

Polyfluorophore excimers and exciplexes as FRET donors in DNA

We describe studies aimed at testing whether oligomeric exciplex and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Forster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3' end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Forster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single wavelength; thus, ODFs may be candidates as "universal FRET donors", thus allowing multicolor FRET of multiple species to be carried out with one excitation.

Prototropic equilibria in DNA containing one-electron oxidized GC: intra-duplex vs. duplex to solvent deprotonation

By use of ESR and UV-vis spectral studies, this work identifies the protonation states of one-electron oxidized G:C (viz. G˙+:C, G(N1–H)˙:C(+H+), G(N1–H)˙:C, and G(N2-H)˙:C) in a DNA oligomer d[TGCGCGCA]2. Benchmark ESR and UV-vis spectra from one electron oxidized 1-Me-dGuo are employed to analyze the spectral data obtained in one-electron oxidized d[TGCGCGCA]2 at various pHs. At pH ≥7, the initial site of deprotonation of one-electron oxidized d[TGCGCGCA]2 to the surrounding solvent is found to be at N1 forming G(N1–H)˙:C at 155 K. However, upon annealing to 175 K, the site of deprotonation to the solvent shifts to an equilibrium mixture of G(N1–H)˙:C and G(N2–H)˙:C. For the first time, the presence of G(N2–H)˙:C in a ds DNA-oligomer is shown to be easily distinguished from the other prototropic forms, owing to its readily observable nitrogen hyperfine coupling (Azz(N2) = 16 G). In addition, for the oligomer in H2O, an additional 8 G N2–H proton HFCC is found. This ESR identification is supported by a UV-vis absorption at 630 nm which is characteristic for G(N2–H)˙ in model compounds and oligomers. We find that the extent of photo-conversion to the C1′ sugar radical (C1′˙) in the one-electron oxidized d[TGCGCGCA]2 allows for a clear distinction among the various G:C protonation states which can not be easily distinguished by ESR or UV-vis spectroscopies with this order for the extent of photo-conversion: G˙+:C > G(N1–H)˙:C(+H+) ≫ G(N1–H)˙:C. We propose that it is the G˙+:C form that undergoes deprotonation at the sugar and this requires reprotonation of G within the lifetime of exited state

UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases

Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)(4), and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.

Enzymatic signal amplification of molecular beacons for sensitive DNA detection

Molecular beacons represent a new family of fluorescent probes for nucleic acids, and have found broad applications in recent years due to their unique advantages over traditional probes. Detection of nucleic acids using molecular beacons has been based on hybridization between target molecules and molecular beacons in a 1:1 stoichiometric ratio. The stoichiometric hybridization, however, puts an intrinsic limitation on detection sensitivity, because one target molecule converts only one beacon molecule to its fluorescent form. To increase the detection sensitivity, a conventional strategy has been target amplification through polymerase chain reaction. Instead of target amplification, here we introduce a scheme of signal amplification, nicking enzyme signal amplification, to increase the detection sensitivity of molecular beacons. The mechanism of the signal amplification lies in target-dependent cleavage of molecular beacons by a DNA nicking enzyme, through which one target DNA can open many beacon molecules, giving rise to amplification of fluorescent signal. Our results indicate that one target DNA leads to cleavage of hundreds of beacon molecules, increasing detection sensitivity by nearly three orders of magnitude. We designed two versions of signal amplification. The basic version, though simple, requires that nicking enzyme recognition sequence be present in the target DNA. The extended version allows detection of target of any sequence by incorporating rolling circle amplification. Moreover, the extended version provides one additional level of signal amplification, bringing the detection limit down to tens of femtomolar, nearly five orders of magnitude lower than that of conventional hybridization assay.

The oxidation potential of adenosine and adenosine-thymidine base pair in chloroform solution

The oxidation potential of 2',3'-O-isopropylidene-5'-O-(tert-butyldimethylsilyl)adenosine and its change upon pairing with the complementary base thymidine have been studied in chloroform solution by voltammetric methods. Differential pulse and cyclic voltammetry of an equimolar solution of the two nucleosides show two well-resolved peaks, which have been assigned to the formation of a H-bonded complex between the two nucleosides and to the fraction of unassociated adenosine in solution. No signal for thymidine oxidation has been detected. Equilibrium constants and enthalpy and entropy changes for self- and hetero-association in solution have been determined by NMR spectra. Quantum mechanical computations show that Hoogsteen and Watson-Crick association modes are of comparable stability in solution, and exhibit very similar oxidation potential in chloroform.

Electronic interactions between pi-stacked chromophores in nonsymmetric tertiary naphthyl di- and polyarylureas

The synthesis, structure, and spectroscopy of a family of tertiary di- and polyarylureas possessing a naphthyl and several different arene end groups separated by a variable number of internal phenylenediamine linking groups are reported. Molecular modeling and (1)H NMR chemical shift data are consistent with the formation of compact, folded structures in which the arene groups adopt a splayed face-to-face geometry. The structure and solvent dependence of the electronic absorption and emission spectra have been determined and are interpreted with the aid of ZINDO calculations. The electronic absorption spectra are relatively insensitive to the choice of arene end group, the number of linking groups, and the solvent polarity. In contrast, the solution fluorescence is highly dependent upon the structure and solvent polarity. These observations are attributed to a small change in polarity upon excitation of the ground state to a naphthalene-localized Franck-Condon singlet state, which can undergo relaxation to a highly polar emissive state with extensive charge-transfer character.

Structure of Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations

Chromophore-DNA complexes are useful for understanding charge transport along pi-stacks once their structural properties have been clarified. We studied two rhodamine 6G semicapping complexes with 15-mer B-DNA duplexes to determine the preferred orientation of the dye with respect to the neighboring base pair. For each of these systems, two distinct chromophore alignments were identified and quantified in terms of base-step parameters. The obtained geometries agree well with those derived from an NMR structure refinement of similar complexes. Cross-correlation analysis of the base-step parameters shows that slide and twist are highly interdependent during the structural transition from one conformation to the other.

The structure of LNA:DNA hybrids from molecular dynamics simulations: the effect of locked nucleotides

Locked nucleic acids (LNAs) exhibit a modified sugar fragment that is restrained to the C3'-endo conformation. LNA-containing duplexes are rather stable and have a more rigid structure than DNA duplexes, with a propensity for A-conformation of the double helix. To gain detailed insight into the local structure of LNA-modified DNA oligomers (as a foundation for subsequent exploration of the electron-transfer capabilities of such modified duplexes), we carried out molecular dynamics simulations on a set of LNA:DNA 9-mer duplexes and analyzed the resulting structures in terms of base step parameters and the conformations of the sugar residues. The perturbation introduced by a single locked nucleotide was found to be fairly localized, extending mostly to the first neighboring base pairs; such duplexes featured a B-type helix. With increasing degree of LNA modification the structure gradually changed; the duplex with one complete LNA strand assumed a typical A-DNA structure. The relative populations of the sugar conformations agreed very well with NMR data, lending credibility to the validity of the computational protocol.

Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA

We propose a lattice fermion model suitable for studying the ultrafast photoexcitation dynamics of ordered chains of deoxyribonucleic acid (DNA) polymers. The model includes both parallel (intrachain) and perpendicular (cross-chain) terms as well as diagonal cross-chain terms coupling neighboring bases. The general form of our Hamiltonian is borrowed from lattice fermion models of quantum chromodynamics. The band structure for this model can be determined analytically, and we use this as a basis for computing the singly excited states of the poly(dA)poly(dT) DNA duplex using configuration interaction singles. Parameters for the model are taken from various literature sources and our own ab initio calculations. Results indicate that the excited states consist of a low energy band of dark charge-separated states followed by separate bands of delocalized excitonic states which have weak mixing between the thymidine and adenosine sides of the DNA chain. We then propose a lattice exciton model based upon the transition dipole-dipole couplings between bases and compare the analytical results for the survival probability of an initially localized exciton to exact numerical results. The results herein underscore the competing role of excitonic and charge-transfer dynamics in these systems.

DNA binding studies of a new dicationic porphyrin. Insights into interligand interactions

Cationic porphyrins have an affinity for DNA and potential for applications in the fields of photodynamic therapy and cellular imaging. This report describes a new dicationic porphyrin, 5,15-dimethyl-10,20-di(N-methylpyridinium-4-yl)porphyrin, abbreviated H2tMe2D4. Although tetrasubstituted, H2tMe2D4 presents modest steric requirements and forms in reasonable yield by a "2+2" synthetic method. Accordingly, studies of the zinc(II)- and copper(II)-containing derivatives, Zn(tMe2D4) and Cu(tMe2D4), have also been possible. Methods used to characterize DNA-binding motifs include absorption, emission, linear, and circular dichroism spectroscopies, as well as viscometry. An unusually detailed picture of porphyrin uptake emerges. As the ratio of DNA to porphyrin increases during a typical titration, H2tMe2D4 or Cu(tMe2D4) initially aggregates on the host and then shifts to intercalative binding at close quarters before finally dispersing into non-interacting intercalation sites of the host. Emission studies of the copper(II) porphyrin have been very valuable. The existence of a measurable signal is diagnostic of intercalative binding, and the saturation behavior establishes that internalization typically monopolizes approximately three base pairs. In the moderate loading regime, emission data are most telling because dipole-dipole interactions between near-neighbor porphyrins tend to confuse other spectroscopic assays. The third ligand, Zn(tMe2D4), behaves differently in that the uptake is a strictly cooperative process. The mode of binding also varies with the base content of the DNA host. When the DNA is rich in A=T base pairs, the porphyrin remains five-coordinate and binds externally; however, Zn(tMe2D4) loses its axial ligand and binds by intercalation if the host contains only G[triple bond]C base pairs.

Sugar radicals formed by photoexcitation of guanine cation radical in oligonucleotides

This work presents evidence that photoexcitation of guanine cation radical (G+*) in dGpdG and DNA-oligonucleotides TGT, TGGT, TGGGT, TTGTT, TTGGTT, TTGGTTGGTT, AGA, and AGGGA in frozen glassy aqueous solutions at low temperatures leads to hole transfer to the sugar phosphate backbone and results in high yields of deoxyribose radicals. In this series of oligonucleotides, we find that G+* on photoexcitation at 143 K leads to the formation of predominantly C5'* and C1'* with small amounts of C3'*. Photoconversion yields of G+* to sugar radicals in oligonucleotides decreased as the overall chain length increased. However, for high molecular weight dsDNA (salmon testes) in frozen aqueous solutions, substantial conversion of G+* to C1'* (only) sugar radical is still found (ca. 50%). Within the cohort of sugar radicals formed, we find a relative increase in the formation of C1'* with length of the oligonucleotide, along with decreases in C3'* and C5'*. For dsDNA in frozen solutions, only the formation of C1'* is found via photoexcitation of G+*, without a significant temperature dependence (77-180 K). Long wavelength visible light (>540 nm) is observed to be about as effective as light under 540 nm for photoconversion of G+* to sugar radicals for short oligonucleotides but gradually loses effectiveness with chain length. This wavelength dependence is attributed to base-to-base hole transfer for wavelengths >540 nm. Base-to-sugar hole transfer is suggested to dominate under 540 nm. These results may have implications for a number of investigations of hole transfer through DNA in which DNA holes are subjected to continuous visible illumination.

Determination of Redox Potentials for the Watson−Crick Base Pairs, DNA Nucleosides, and Relevant Nucleoside Analogues

Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.

Photoexcitation of dinucleoside radical cations: a time-dependent density functional study

The excited states of dinucleoside phosphates (dGpdG, dApdA, dApdT, TpdA, and dGpdT) in their cationic radical states were studied with time-dependent density functional theory (TD-DFT). The ground-state geometries of all the dinucleoside phosphate cation radicals considered, in their base stacked conformation, were optimized with the B3LYP/6-31G(d) method. Further, to take into account the effect of the aqueous environment surrounding the dinucleoside phosphates, the polarized continuum model (PCM) was considered and the excitation energies were computed by using the TD-B3LYP/6-31G(d) method. From this study, we find that the first transition in all the dinucleoside molecules involves hole transfer from base to base. dG*+pdG and dApdA*+ were found to have substantially lower first transition energies than others with two different DNA bases. Higher energy transitions involve base to sugar as well as base to base hole transfer. The calculated TD-B3LYP/6-31G(d) transition energies are in good agreement with previous calculations with CASSCF/CAS-PT2 level of theory. This TD-DFT work supports the experimental findings that sugar radicals formed upon photoexcitation of G*+ in gamma-irradiated DNA and suggests an explanation for the wavelength dependence found.

Successive Attachment of Electrons to Protonated Guanine: (G+H)• Radicals and (G+H)- Anions

The structures, energetics, and vibrational frequencies of nine hydrogenated 9H-keto-guanine radicals (G+H)(*) and closed-shell anions (G+H)(-) are predicted using the carefully calibrated (Chem. Rev. 2002, 102, 231) B3LYP density functional method in conjunction with a DZP++ basis set. These radical and anionic species come from consecutive electron attachment to the corresponding protonated (G+H)(+) cations in low pH environments. The (G+H)(+) cations are studied using the same level of theory. The proton affinity (PA) of guanine computed in this research (228.1 kcal/mol) is within 0.7 kcal/mol of the latest experiment value. The radicals range over 41 kcal/mol in relative energy, with radical r1, in which H is attached at the C8 site of guanine, having the lowest energy. The lowest energy anion is a2, derived by hydride ion attachment at the C2 site of guanine. No stable N2-site hydride should exist in the gas phase. Structure a9 was predicted to be dissociative in this research. The theoretical adiabatic electron affinities (AEA), vertical electron affinities, and vertical detachment energies were computed, with AEAs ranging from 0.07 to 3.12 eV for the nine radicals.

Role of the guanine N1 imino proton in the migration and reaction of radical cations in DNA oligomers

Oxidation of a guanine nucleobase to its radical cation in DNA oligomers causes an increase in the acidity of the N1 imino proton that may lead to its spontaneous transfer to N3 of the paired cytosine. This proton transfer is suspected of playing an important role in long-distance radical cation hopping in DNA and the decisive product-determining role in the reaction of the radical cation with H2O or O2. We prepared and investigated DNA oligomers in which certain deoxycytidines are replaced by 5-fluoro-2'-deoxycytidines (F5dC). The pKa of F5C was determined to be 1.7 units below that of dC, which causes proton transfer from the guanine radical cation to be thermodynamically unfavorable. Photoinitiated one-electron oxidation of the DNA by UV irradiation of a covalently attached anthraquinone derivative introduces a radical cation that hops throughout the oligomer and is trapped selectively at GG steps. The introduction of F5dC does not affect the efficiency of charge hopping, but it significantly reduces the amount of reaction at the GG sites, as revealed by subsequent reaction with formamidopyrimidine glycosylase. These findings suggest that transfer of the guanine radical cation N1 proton to cytosine does not play a significant role in long-range charge transfer, but this process does influence the reactions with H2O and/or O2.