A Twisting Electronic Nanoswitch Made of DNA

Single‐stranded DNAs and RNAs that are rich in the nucleobase guanine form four‐stranded G‐quadruplexes, which are held together by hydrogen‐bonded guanine quartets. In aqueous solution, both DNA duplexes and G‐quadruplexes are modest conductors of electrical charge. A tight, topologically constrained DNA construct called twDNA is now reported, in which a core of four guanine‐rich single strands structurally and electronically links together four DNA double helices. The addition and removal of K⁺ or Sr²⁺ cations promote alternative conformers of twDNA, which have strikingly distinct electronic properties. Unlike DNA mechano‐electronic switches that require large conformational changes, twDNA requires only modest twisting/untwisting structural attenuations to achieve electronic switching.     

UV‐Light‐Induced Hydrogen Transfer in Guanosine–Guanosine Aggregates

Aggregates of a lipophilic guanine (G) derivative have been studied in n‐hexane by femtosecond‐to‐microsecond UV‐visible broadband transient absorption, stationary infrared and UV‐visible spectroscopy and by quantum chemical calculations. We report the first time‐resolved spectroscopic detection of hydrogen transfer in GG aggregates, which leads to (G?H) ^. radicals by means of G⁺G^? charge transfer followed by proton transfer. These radicals show a characteristic electronic spectrum in the range 300–550 nm. The calculated superimposed spectrum of the species that result from NH???N proton transfer agrees best with the experimental spectrum.     

Thermolysis of 3‐alkyl‐3‐methyl‐1,2‐dioxetanes: activation parameters and chemiexcitation yields

3‐Methyl‐3‐(3‐pentyl)‐1,2‐dioxetane 1 and 3‐methyl‐3‐(2,2‐dimethyl‐1‐propyl)‐1,2‐dioxetane 2 were synthesized in low yield by the α‐bromohydroperoxide method. The activation parameters were determined by the chemiluminescence method (for 1 ΔH‡ = 25.0 ± 0.3 kcal/mol, ΔS‡ = −1.0 entropy unit (e.u.), ΔG‡ = 25.3 kcal/mol, k₁ (60°C) = 4.6 × 10⁻⁴s⁻¹; for 2 ΔH‡ = 24.2 ± 0.2 kcal/mol, ΔS‡ = −2.0 e.u., ΔG‡ = 24.9 kcal/mol, k₁ (60°C) = 9.2 × 10⁻⁴s⁻¹. Thermolysis of 1–2 produced excited carbonyl fragments (direct production of high yields of triplets relative to excited singlets) (chemiexcitation yields for 1: ϕ^T = 0.02, ϕ^S ≤ 0.0005; for 2: ϕ^T = 0.02, ϕ^S ≤ 0.0004). The results are discussed in relation to a diradical‐like mechanism. © 2001 John Wiley & Sons, Inc. Heteroatom Chem 12:176–179, 2001     

Theoretical study on the degradation mechanism of methamidophos and chloramine phosphorus with OH radicals

Theoretical investigation on the gas‐phase degradation reaction mechanism of methamidophos (MAP) and chloramine phosphorus (CHP) with OH radicals is performed. The equilibrium geometries and the harmonic vibration frequencies of the stationary points are obtained at M06‐2x/6‐31+G(d,p) level, and the higher‐level energetic information is further refined at M06‐2x/6–311++G(3df,2p) level. The rate constants for the 14 reaction channels are calculated by the improved canonical variational transition state theory with small‐curvature tunneling correction over the temperature range 200–2000 K. The three‐parameter expressions of k₁(T) = 1.53 × 10^?19T^2.74exp(?1005.12/T), k₂(T) = 1.36 × 10^?20T^3.02exp(?1259.56/T) are given. The total rate constants of all reaction channels of MAP with OH radicals are in good agreement with the available experimental data. Our results indicate that the H‐abstraction reactions on methyl are the major channels for the reaction of MAP and CHP with OH radicals. © 2015 Wiley Periodicals, Inc.     

Generation and EPR Spectroscopy of the First Silenyl Radicals,R2C=Si.−R: Experiment and Theory

The first two persistent silenyl radicals (R₂C=Si^.?R), with a half‐life (t_1/2) of about 30 min, were generated and characterized by electron paramagnetic resonance (EPR) spectroscopy. The large hyperfine coupling constants (hfccs) (a(²⁹Si_α)=137.5–148.0 G) indicate that the unpaired electron has substantial s character. DFT calculations, which are in good agreement with the experimentally observed hfccs, predict a strongly bent structure (?C=Si?R=134.7–140.7°). In contrast, the analogous vinyl radical, R₂C=C^.?R (t_1/2≈3 h), exhibits a small hfcc (a(¹³C_α)=26.6 G) and has a nearly linear geometry (?C=C?R=168.7°).     

Generation and EPR Spectroscopy of the First Silenyl Radicals,R2C=Si.−R: Experiment and Theory

The first two persistent silenyl radicals (R₂C=Si^.?R), with a half‐life (t_1/2) of about 30 min, were generated and characterized by electron paramagnetic resonance (EPR) spectroscopy. The large hyperfine coupling constants (hfccs) (a(²⁹Si_α)=137.5–148.0 G) indicate that the unpaired electron has substantial s character. DFT calculations, which are in good agreement with the experimentally observed hfccs, predict a strongly bent structure (?C=Si?R=134.7–140.7°). In contrast, the analogous vinyl radical, R₂C=C^.?R (t_1/2≈3 h), exhibits a small hfcc (a(¹³C_α)=26.6 G) and has a nearly linear geometry (?C=C?R=168.7°).     

Generation of 8‐oxo‐7,8‐dihydroguanine in G‐Quadruplexes Models of Human Telomere Sequences by One‐electron Oxidation

The mechanistic aspects of one‐electron oxidation of G‐quadruplexes in the basket (Na⁺ ions) and hybrid (K⁺ ions) conformations were investigated by transient absorption laser kinetic spectroscopy and HPLC detection of the 8‐oxo‐7,8‐dihydroguanine (8‐oxoG) oxidation product. The photo‐induced one‐electron abstraction from G‐quadruplexes was initiated by sulfate radical anions (SO₄˙^?) derived from the photolysis of persulfate ions by 308 nm excimer laser pulses. In neutral aqueous solutions (pH 7.0), the transient absorbance of neutral guanine radicals, G(‐H)˙, is observed following the complete decay of SO₄˙^? radicals (~10 μs after the actinic laser flash). In both basket and hybrid conformations, the G(‐H)˙ decay is biphasic with one component decaying with a lifetime of ~0.1 ms, and the other with a lifetime of 20–30 ms. The fast decay component (~0.1 ms) in G‐quadruplexes is correlated with the formation of 8‐oxoG lesions. We propose that in G‐quadruplexes, G(‐H)˙ radicals retain radical cation character by sharing the N1‐proton with the O⁶‐atom of G in the [G˙⁺: G] Hoogsteen base pair; this [G(‐H)˙: H⁺G G˙⁺: G] leads to the hydration of G˙⁺ radical cation within the millisecond time domain, and is followed by the formation of the 8‐oxoG lesions.     

Proton‐Coupled Electron Transfer of Unsaturated Fatty Acids and Mechanistic Insight into Lipoxygenase

A proton‐coupled electron transfer (PCET) process plays an important role in the initial step of lipoxygenases to produce lipid radicals which can be oxygenated by reaction with O₂ to yield the hydroperoxides stereoselectively. The EPR spectroscopic detection of free lipid radicals and the oxygenated radicals (peroxyl radicals) together with the analysis of the EPR spectra has revealed the origin of the stereo‐ and regiochemistry of the reaction between O₂ and linoleyl (= (2Z)‐10‐carboxy‐1‐[(1Z)‐hept‐1‐enyl]dec‐2‐enyl) radical in lipoxygenases. The direct determination of the absolute rates of H‐atom‐transfer reactions from a series of unsaturated fatty acids to the cumylperoxyl (= (1‐methyl‐1‐phenylethyl)dioxy) radical by use of time‐resolved EPR at low temperatures together with detailed kinetic investigations on both photoinduced and thermal electron‐transfer oxidation of unsaturated fatty acids provides the solid energetic basis for the postulated PCET process in lipoxygenases. A strong interaction between linoleic acid (= (9Z,12Z)‐octadeca‐9,12‐dienoic acid) and the reactive center of the lipoxygenases (Fe^III? OH) is suggested to be involved to make a PCET process to occur efficiently, when an inner‐sphere electron transfer from linoleic acid to the Fe^III state is strongly coupled with the proton transfer to the OH group.     

Multi‐faceted Reactivity of Alkyltellurophenols Towards Peroxyl Radicals: Catalytic Antioxidant Versus Thiol‐Depletion Effect

Hydroxyaryl alkyl tellurides are effective antioxidants both in organic solution and aqueous biphasic systems. They react by an unconventional mechanism with ROO^. radicals with rate constants as high as 10⁷ M ^?1 s^?1 at 303 K, outperforming common phenols. The reactions proceed by oxygen atom transfer to tellurium followed by hydrogen atom transfer to the resulting RO^. radical from the phenolic OH. The reaction rates do not reflect the electronic properties of the ring substituents and, because the reactions occur in a solvent cage, quenching is more efficient when the OH and TeR groups have an ortho arrangement. In the presence of thiols, hydroxyaryl alkyl tellurides act as catalytic antioxidants towards both hydroperoxides (mimicking the glutathione peroxidases) and peroxyl radicals. The high efficiency of the quenching of the peroxyl radicals and hydroperoxides could be advantageous under normal cellular conditions, but pro‐oxidative (thiol depletion) when thiol concentrations are low.     

Site-specific control of N7-metal coordination in DNA by a fluorescent purine derivative

A synthetic strategy that utilizes O6‐protected 8‐bromoguanosine gives broad access to C8‐guanine derivatives with phenyl, pyridine, thiophene, and furan substituents. The resulting 8‐substituted 2′‐deoxyguanosines are push–pull fluorophores that can exhibit environmentally sensitive quantum yields (Φ=0.001–0.72) due to excited‐state proton‐transfer reactions with bulk solvent. Changes in nucleoside fluorescence were used to characterize metal‐binding affinity and specificity of 8‐substituted 2′‐deoxyguanosines. One derivative, 8‐(2‐pyridyl)‐2′‐deoxyguanosine (2PyG), exhibits selective binding of Cu^II, Ni^II, Cd^II, and Zn^II through a bidentate effect provided by the N7 position of guanine and the 2‐pyridyl nitrogen atom. Upon incorporation into DNA, 2‐pyridine‐modified guanine residues selectively bind to Cu^II and Ni^II with equilibrium dissociation constants (K_d) that range from 25 to 850 nM ; the affinities depend on the folded state of the oligonucleotide (duplex>G‐quadruplex) as well as the identity of the metal ion (Cu>Ni?Cd). These binding affinities are approximately 10 to 1 000 times higher than for unmodified metal binding sites in DNA, thereby providing site‐specific control of metal localization in alternatively folded nucleic acids. Temperature‐dependent circular‐dichroism studies reveal metal‐dependent stabilization of duplexes, but destabilization of G‐quadruplex structures upon adding Cu^II to 2PyG‐modified oligonucleotides. These results demonstrate how the addition of a single pyridine group to the C8 position of guanine provides a powerful new tool for studying the effects of N7 metalation on the structure, stability, and electronic properties of nucleic acids.     

Reversible pH Switch of Two‐Quartet G‐Quadruplexes Formed by Human Telomere

A four‐repeat human telomere DNA sequence without the 3′‐end guanine, d[TAGGG(TTAGGG)₂TTAGG] (htel1‐ΔG23) has been found to adopt two distinct two G‐quartet antiparallel basket‐type G‐quadruplexes, TD and KDH⁺ in presence of KCl. NMR, CD, and UV spectroscopy have demonstrated that topology of KDH⁺ form is distinctive with unique protonated T18?A20⁺?G5 base triple and other capping structural elements that provide novel insight into structural polymorphism and heterogeneity of G‐quadruplexes in general. Specific stacking interactions amongst two G‐quartets flanking base triples and base pairs in TD and KDH⁺ forms are reflected in 10 K higher thermal stability of KDH⁺. Populations of TD and KDH⁺ forms are controlled by pH. The (de)protonation of A20 is the key for pH driven structural transformation of htel1‐ΔG23. Reversibility offers possibilities for its utilization as a conformational switch within different compartments of living cell enabling specific ligand and protein interactions.     

Photosensitized oxidative DNA damage: from hole injection to chemical product formation and strand cleavage

Oxidatively generated damage to DNA induced by a pyrenyl photosensitizer residue (Py) covalently attached to a guanine base in the DNA sequence context 5'-d(CAT[G1Py]CG2TCCTAC) in aerated solutions was monitored from the initial one-electron transfer, or hole injection step, to the formation of chemical end-products monitored by HPLC, mass spectrometry, and high-resolution gel electrophoresis. Hole injection into the DNA was initiated by two-photon excitation of the Py residue with 355 nm laser pulses, thus producing the radical cation Py*+ and hydrated electrons; the latter are trapped by O2, thus forming the superoxide anion O2*-. The decay of the Py*+ radical is correlated with the appearance of the G*+/G(-H)* radical on microsecond time scales, and O2*- combines with guanine radicals at G1 to form alkali-labile 2,5-diamino-4H-imidazolone lesions (Iz1Py). Product formation in the modified strand is smaller by a factor of 2.4 in double-stranded than in single-stranded DNA. In double-stranded DNA, hot piperidine-mediated cleavage at G2 occurs only after G1Py, an efficient hole trap, is oxidized thus generating tandem lesions. An upper limit of hole hopping rates, khh < 5 x 103 s-1 from G1*+-Py to G2 can be estimated from the known rates of the combination reaction of the G(-H)* and O2*- radicals. The formation of Iz products in the unmodified complementary strand compared to the modified strand in the duplex is approximately 10 times smaller. The formation of tandem lesions is observed even at low levels of irradiation corresponding to "single-hit" conditions when less than approximately 10% of the oligonucleotide strands are damaged. A plausible mechanism for this observation is discussed.     

A Remarkable Solvent Effect on the Nuclearity of Neutral Titanium(IV)‐Based Helicate Assemblies

The spontaneous self‐assembly of a neutral circular trinuclear Ti^IV‐based helicate is described through the reaction of titanium(IV) isopropoxide with a rationally designed tetraphenolic ligand. The trimeric ring helicate was obtained after diffusion of n‐pentane into a solution with dichloromethane. The circular helicate has been characterized by using single‐crystal X‐ray diffraction study, ¹³C CP‐MAS NMR and ¹H NMR DOSY solution spectroscopic, and positive electrospray ionization mass‐spectrometric analysis. These analytical data were compared with those obtained from a previously reported double‐stranded helicate that crystallizes in toluene. The trimeric ring was unstable in a pure solution with dichloromethane and transformed into the double‐stranded helicate. Thermodynamic analysis by means of the PACHA software revealed that formation of the double‐stranded helicates was characterized by ΔH(toluene)=?30 kJ mol^?1 and ΔS(toluene)=+357 J K^?1 mol^?1, whereas these values were ΔH(CH₂Cl₂)=?75 kJ mol^?1 and ΔS(CH₂Cl₂)=?37 J K^?1 mol^?1 for the ring helicate. The transformation of the ring helicate into the double‐stranded helicate was a strongly endothermic process characterized by ΔH(CH₂Cl₂)=+127 kJ mol^?1 and ΔH(n‐pentane)=+644 kJ mol^?1 associated with a large positive entropy change ΔS=+1115 J K^?1?mol^?1. Consequently, the instability of the ring helicate in pure dichloromethane was attributed to the rather high dielectric constant and dipole moment of dichloromethane relative to n‐pentane. Suggestions for increasing the stability of the ring helicate are given.     

Label‐Free Photoelectrochemical Detection of Double‐Stranded HIV DNA by Means of a Metallointercalator‐Functionalized Electrogenerated Polymer

The design of photoactive functionalized electrodes for the sensitive transduction of double‐stranded DNA hybridization is reported. Multifunctional complex [Ru(bpy‐pyrrole)₂(dppn)]²⁺ (bpy‐pyrrole=4‐methyl‐4′‐butylpyrrole‐2,2′‐bipyridine, dppn=benzo[i]dipyrido[3,2‐a:2′,3′‐c]phenazine) exhibiting photosensitive, DNA‐intercalating, and electropolymerizable properties was synthesized and characterized. The pyrrole groups undergo oxidative electropolymerization on planar electrodes forming a metallopolymer layer on the electrode. Thanks to the photoelectrochemical and intercalating properties of the immobilized Ru^II complex, the binding of a double‐stranded HIV DNA target was photoelectrochemically detected on planar electrodes. Photocurrent generation through visible irradiation was correlated to the interaction between double‐stranded DNA and the metallointercalator polymer. These interactions were well fitted by using a Langmuir isotherm, which allowed a dissociation constant of 2×10⁶ L mol^?1 to be estimated. The low detection limit of 1 fmol L^?1 and sensitivity of 0.01 units per decade demonstrate excellent suitability of these modified electrodes for detection of duplex DNA.     

Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-aza-7-deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet†

The guanine derivative, 5-aza-7-deazaguanine (^5N7CG) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art extended multi-state complete active space second-order perturbation theory. It is demonstrated that excitation to the lowest energy ¹ππ* state of ^5N7CG results in complex dynamics leading to ca. 10- to 30-fold slower relaxation (depending on solvent) compared with guanine. A significant conformational change occurs at the S₁ minimum, resulting in a 10-fold greater fluorescence quantum yield compared with guanine. The fluorescence quantum yield and S₁ decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S₁ minimum and the S₁/S₀ conical intersection going from water to propanol. The longer lifetimes might make ^5N7CG more photochemically active to adjacent nucleobases than guanine or other nucleobases within DNA.     

Duplex‐Selective Ruthenium‐Based DNA Intercalators

We report the design and synthesis of small molecules that exhibit enhanced luminescence in the presence of duplex rather than single‐stranded DNA. The local environment presented by a well‐known [Ru(dipyrido[3,2‐a:2′,3′‐c]phenazine)L₂]²⁺‐based DNA intercalator was modified by functionalizing the bipyridine ligands with esters and carboxylic acids. By systematically varying the number and charge of the pendant groups, it was determined that decreasing the electrostatic interaction between the intercalator and the anionic DNA backbone reduced single‐strand interactions and translated to better duplex specificity. In studying this class of complexes, a single Ru^II complex emerged that selectively luminesces in the presence of duplex DNA with little to no background from interacting with single‐stranded DNA. This complex shows promise as a new dye capable of selectively staining double‐ versus single‐stranded DNA in gel electrophoresis, which cannot be done with conventional SYBR dyes.     

Application of spin trapping to redox-initiated vinyl polymerization with thiourea as the reductant

An electron spin resonance (ESR) study confirms a free radical mechanism for aqueous vinyl polymerization initiated by three redox systems involving thiourea. The primary radical, NH₂? C (?NH)S^., could not be detected by ESR spectroscopy, perhaps because of its large g anisotropy and/or very short relaxation time. Propagating radicals are trapped from methyl-methacrylate by 2-methyl-2-nitroso propane (MNP) and their structures are found to be the same as those produced by either azo-bis-isobutyrnitrile or di-t-butyl peroxylate. The latter monomer, however, reacts with MNP in the absence of any initiator, giving different ESR lines.     

Structural characterization of ether lipids from the archaeon Sulfolobus islandicus by high‐resolution shotgun lipidomics

The molecular structures, biosynthetic pathways and physiological functions of membrane lipids produced by organisms in the domain Archaea are poorly characterized as compared with that of counterparts in Bacteria and Eukaryota. Here we report on the use of high‐resolution shotgun lipidomics to characterize, for the first time, the lipid complement of the archaeon Sulfolobus islandicus. To support the identification of lipids in S. islandicus, we first compiled a database of ether lipid species previously ascribed to Archaea. Next, we analyzed the lipid complement of S. islandicus by high‐resolution Fourier transform mass spectrometry using an ion trap‐orbitrap mass spectrometer. This analysis identified five clusters of molecular ions that matched ether lipids in the database with sub‐ppm mass accuracy. To structurally characterize and validate the identities of the potential lipid species, we performed structural analysis using multistage activation on the ion trap‐orbitrap instrument as well as tandem mass analysis using a quadrupole time‐of‐flight machine. Our analysis identified four ether lipid species previously reported in Archaea, and one ether lipid species that had not been described before. This uncharacterized lipid species features two head group structures composed of a trisaccharide residue carrying an uncommon sulfono group (?SO₃) and an inositol phosphate group. Both head groups are linked to a glycerol dialkyl glycerol tetraether core structure having isoprenoid chains with a total of 80 carbon atoms and 4 cyclopentane moieties. The shotgun lipidomics approach deployed here defines a novel workflow for exploratory lipid profiling of Archaea. Copyright © 2015 John Wiley & Sons, Ltd.     

Interaction of zinc oxide clusters with molecules related to the sulfur vulcanization of polyolefins ("rubber")

The vulcanization of rubber by sulfur is a large‐scale industrial process that is only poorly understood, especially the role of zinc oxide, which is added as an activator. We used the highly symmetrical cluster Zn₄O₄ (T_d) as a model species to study the thermodynamics of the initial interaction of various vulcanization‐related molecules with ZnO by DFT methods, mostly at the B3LYP/6‐31+G* level. The interaction energy of Lewis bases with Zn₄O₄ increases in the following order: CO62H₄3H₆2S₂<1,4‐C₅H₈2O2S3N?CH₃COO^?. The corresponding binding energies range from ?57 to ?262 kJ mol^?1. However, Brønsted acids react with the Zn₄O₄ cluster with proton transfer from the ligand molecule to one of the oxygen atoms of Zn₄O₄, and these reactions are all strongly exothermic [binding energies [kJ mol^?1] in parentheses: H₂O (?183), MeOH (?171), H₂S (?245), MeSH (?230), C₃H₆ (?121), and CH₃COOH (?255)]. The important vulcanization accelerator mercaptobenzothiazole (C₇H₅NS₂, MBT) containing several donor sites reacts with the Zn₄O₄ cluster with proton transfer from the NH group to one of the oxygen atoms of ZnO, and in addition the exocyclic thiono sulfur atom and the nitrogen atom coordinate to one and the same zinc atom, resulting in a binding energy of ?247 kJ mol^?1. A second isomer of [(MBT)Zn₄O₄] with a strong O? H???N hydrogen bond rather than a Zn? N bond is only slightly less stable (binding energy ?243 kJ mol^?1). The NH form of free MBT is 36 kJ mol^?1 more stable than the tautomeric SH form, while the sulfurized MBT derivative benzothiazolyl hydrodisulfide C₇H₅NS₃ (BtSSH) is most stable with the connectivity >CSSH.