Aminoglycoside (neomycin) preference is for A-form nucleic acids,not just RNA: results from a competition dialysis study

Aminoglycosides have been at the forefront of antimicrobial therapy for the past 50 years. Their specificity is believed to lie in binding duplex RNAs (rRNA). Competition dialysis studies of various nucleic acid forms with 9-aminoacridine, quinacrine, and a neomycin-acridine conjugate were carried out. Our results suggest a strong preference for aminoglycoside binding to nucleic acids that can adopt an A-type conformation. These results challenge the common belief that aminoglycoside specificity is simply for duplex RNAs.     

Excess electron-transfer-based repair of a Cis-Syn thymine dimer in DNA is not sequence dependent

The repair of a cis-syn pyrimidine dimer by single electron reduction is possible in DNA over large distances. The intervening base sequence does not influence the repair yield.     

Oxidative DNA Damage in the Photolysis of Af-Hydroxy-2-Pyridone, a Specific Hydroxyl-Radical Source

Abstract The photooxidative DNA damage by iV-hydroxy-2-pyri-done (1) is caused by hydroxyl radicals, as confirmed by electron paramagnetic resonance studies with the spin trap 5,5-dimethylpyrroline JV-oxide. Irradiation of the pyridone 1 at 300 nm induced strand breaks in super-coiled pBR322 DNA, while in calf-thymus DNA and 2'-deoxyguanosine (dG), respectively, 8-oxoguanine and 8-oxo-7,8-dihydro-2'-deoxyguanosine were formed. Time-dependent control experiments disclosed that photoprod-ucts of pyridone 1, e.g. 2-pyridone (3), are not responsible for the modification of DNA. Also the photosensitization by the pyridine-2-one chromophore was excluded, because JV-methylpyridine-2-one (2), which cannot generate hydroxyl radicals, was ineffective in the photooxidation of DNA and dG. Thus, the photolysis of pyridone 1 serves as a specific source of hydroxyl radicals for DNA damage, both strand breaks and base modifications.     

Oxidation of guanine bases mediated by a manganese-porphyrin-oligonucleotide conjugate onto a G-rich DNA target: 8-oxo-7,8-dihydroguanine is not the major lesion

The oxidative alkali-labile G lesions mediated by manganese porphyrin oligonucleotide conjugate on a DNA target could not be attibuted to the formation of 8-oxo-7,8-dihydroguanine since they were not substrate of the Fpg protein. In order to identify the nature of these lesions, an analysis of the oxidized derivatives of 2′-deoxyguanosine, imidazolone and oxazolone, generated by photooxidation, was efficiently performed by using the positive electrospray ionisation-mass spectrometry method.     

Light-induced Damage in the Retina: Differential Effects of Dimethylthiourea on Photoreceptor Survival, Apoptosis and DNA Oxidation

In the rat, photoreceptor cell death from exposure to intense visible light can be prevented by prior treatment with antioxidants. In this study we subjected albino rats raised in dim cyclic light and rats made more susceptible to light damage by rearing in darkness to exposures of green light that led to similar losses of photoreceptor cells. Rhodopsin and photoreceptor DNA, indicators of the number of surviving photoreceptor cells, were determined at various times over a period of 14 days after light exposure. Fragmentation of DNA was determined over a similar time course by neutral and alkaline agarose gel electrophoresis. Apoptosis in retinal DNA was measured by quantitating the appearance of 180 base pair (bp) nucleosomal fragments. Oxidation of DNA was measured by electrochemical detection of the nucleoside 8-hydroxydeoxyguanosine (8-OHdG) after separation by high-performance chromatography. For albino rats reared in dim cyclic light, 24 h of intense light exposure resulted in the loss of 50% rhodopsin and photoreceptor cell DNA. In dark-reared rats, the losses were 40%, respectively, after only 3 h of intense light treatment. In both cases pretreatment with the antioxidant dimethylthiourea (DMTU) prevented rhodopsin and photoreceptor cell DNA loss. The kinetics of the light-induced apoptosis depended markedly on the rearing environment of the rats. The DNA ladders appeared within 12 h of the onset of intense light in the rats reared in dim cyclic light. In these rats the 180 bp fragment was at two-thirds of its maximum intensity immediately after 24 h of light exposure and reached the maximum 12 h later. Dimethylthiourea partially inhibited ladder formation in rats reared in dim cyclic light and delayed the time of appearance of the 180 bp maximum by 6 h. By contrast, in rats reared in darkness the 180 bp fragment was undetected immediately after 3 h of light exposure and reached its maximum 2 days later. Pretreatment with DMTU completely eliminated DNA ladders in these rats. Alkaline gel electrophoresis revealed a pattern of single-strand DNA breaks, with relatively high molecular weight fragments, 6 h after light exposure of dark-reared rats. Single-strand DNA breaks in cyclic light rats corresponded with the onset of apoptotic ladders, but peak values preceded by 12 h the peak of DNA ladder formation. The quantity of 8-OHdG in retinal DNA remained close to control values in all samples with the exception of a peak of twice the control value 18 h after light exposure in the dark-reared rats and a value 60% higher 16 days after exposure in cyclic light animals. Dimethylthiourea had no effect on the amount of oxidized purine in any of the samples. The differences between dark-reared rats and rats reared in dim cyclic light in the kinetics of DNA fragmentation and in their response to treatment with DMTU is consistent with previous observations of fundamental differences in retinal cell physiology in these animals. In dim light-reared rats, the pathway to apoptosis may be qualitatively different from the pathway to net photoreceptor loss in rats reared in darkness. The lack of effect of DMTU on 8-OHdG formation suggests that the oxidation of DNA bases is not a causal factor in light-mediated photoreceptor cell death.     

A self-assembled cage as a non-covalent protective group: regioselectivity control in the nucleophilic substitution of aryl-substituted allylic chlorides

Aryl-substituted allylic chlorides are accommodated by a self-assembled cage in such a restricted orientation that the internal reaction sites are shielded while the external ones are exposed. This non-covalent protection enhances terminal regioselectivity in the allylic substitution.     

Bulged Guanine is Uniquely Sensitive to Damage Caused by Visible‐Light Irradiation of Ethidium Bound to DNA: A Possible Role in Mutagenesis

The interaction of ethidium bromide (=3,8‐diamino‐5‐ethyl‐6‐phenylphenanthridinium bromide; EB) with a series of duplex DNA oligomers having single‐base bulges and single‐base mis‐pairs was investigated (Fig. 1). Physical and spectroscopic analysis reveals no definitive evidence for selective binding of EB at the bulge or mis‐pair. However, irradiation of the bound EB with VIS light leads to lesions in the DNA selectively in the sequence having a bulged guanine. This reaction is attributed to the formation of an exciplex between the lowest excited singlet state of the EB and the bulged guanine. The exciplex is trapped by H₂O, which initiates a sequence of reactions that lead to piperidine‐requiring strand cleavage at this site. Significantly, the damaged bulged guanine is not recognized by E. coli formamidopyrimidine glycosylase (Fpg), which is part of a base‐excision repair system for oxidative damage to DNA. Thus, DNA containing a bulged guanine and having a bound intercalator may be irreparably damaged by exposure to VIS light, even though normal duplex DNA is relatively inert under these conditions.     

15N NMR study on site-selective binding of metal ions to guanine runs in DNA: a good correlation with HOMO distribution

15N NMR of DNA containing 15N-N7-enriched guanine (G) in the presence of paramagnetic ions (Mn(II) and Co(II)) was investigated. As the concentration of metal ion was increased, 15N NMR signals of the 5'G of GG and the middle G of GGG broadened site-selectively, indicating that electron-donating sites in G runs preferentially localize on the 5'G of GG and the middle G of GGG. The selectivity for G-metal ion interaction observed in this study was in good agreement with calculated HOMO distribution of G runs.     

Circumstances in which radiation is not absorbed, forbidding photoionization: four classes of matrix element zeros

We compare a new class of photoionization matrix element zeros, which we will call relativistic high-energy zeros (RHEZ), occurring at energies on the order mc², to three well-studied classes of zeros, which include Cooper minima, point Coulomb relativistic zeros (PCRZ) and higher energy nonrelativistic Coulomb zeros (HENRCZ). RHEZ differ from the other three types of zeros in several ways. For example, the position of the zero with respect to photon energy in dipole RHEZ matrix elements is completely independent of n, Z, the central potential V, and retardation; has a simple dependence on the bound state l quantum number. Despite the fact that RHEZ occur at such high energies the dipole RHEZ do have some physical consequences.     

Tunable hydrophobicity in DNA micelles: design, synthesis, and characterization of a new family of DNA amphiphiles

This work describes the synthesis and characterization of a new family of DNA amphiphiles containing modified nucleobases. The hydrophobicity was imparted by the introduction of a dodec-1-yne chain at the 5-position of the uracil base, which allowed precise and simple tuning of the hydrophobic properties through solid-phase DNA synthesis. The micelles formed from these modified DNA sequences were characterized by atomic force microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis. These experiments revealed the role of the quantity and location of the hydrophobic units in determining the morphology and stability of the micelles. The effects of hybridization on the physical characteristics of the DNA micelles were also studied; these results showed potential for the sequence-specific noncovalent functionalization of the self-assembled aggregates.     

Damage to DNA in bacterioplankton: a model of damage by ultraviolet radiation and its repair as influenced by vertical mixing

A model of UV-induced DNA damage in oceanic bacterioplankton was developed and tested against previously published and novel measurements of cyclobutane pyrimidine dimers (CPD) in surface layers of the ocean. The model describes the effects of solar irradiance, wind-forced mixing of bacterioplankton and optical properties of the water on net DNA damage in the water column. The biological part includes the induction of CPD by UV radiation and repair of this damage through photoreactivation and excision. The modeled damage is compared with measured variability of CPD in the ocean: diel variation in natural bacterioplankton communities at the surface and in vertical profiles under different wind conditions (net damage as influenced by repair and mixing); in situ incubation of natural assemblages of bacterioplankton (damage and repair, no mixing); and in situ incubation of DNA solutions (no repair, no mixing). The model predictions are generally consistent with the measurements, showing similar patterns with depth, time and wind speed. A sensitivity analysis assesses the effect on net DNA damage of varying ozone thickness, colored dissolved organic matter concentration, chlorophyll concentration, wind speed and mixed layer depth. Ozone thickness and mixed layer depth are the most important factors affecting net DNA damage in the mixed layer. From the model, the total amplification factor (TAF; a relative measure of the increase of damage associated with a decrease in ozone thickness) for net DNA damage in the euphotic zone is 1.7, as compared with 2.1-2.2 for irradiance weighted for damage to DNA at the surface.     

The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures

The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves. We present an analysis of the geometry of ligands bound to proteins and highlight the role of small molecule crystal structures in enabling molecular modellers to critically evaluate a ligand model’s quality and investigate protein-induced strain.     

Adsorption of oxalate on rutile particles in aqueous solutions: a spectroscopic, electron-microscopic and theoretical study

The adsorption of oxalic acid from the aqueous phase at the surface of rutile nanoparticles has been investigated by attenuated total-reflection Fourier-transformed infrared (ATR-FTIR) measurements. A combination of high resolution transmission electron microscopy (HRTEM) and Wulff-type construction was used to elucidate the typical morphology of the nanocrystals. It is estimated that (110)-type facets present more than 85% of the exposed surface in the powder. The aqueous system was also studied quantum-chemically using the semiempirical method MSINDO. Geometry optimizations have been performed, and the vibration spectra of the most stable surface complexes have been calculated. A sequence of model types has been applied in the quantum-chemical calculations in order to take into account the effect of interaction of water and oxalic acid on the adsorption mechanism and the vibration spectra. It was found that the presence of the aqueous phase significantly changes the stability of the oxalic acid surface complexes compared with the bare TiO(2) surface. The combination of experimental and theoretical information allowed identification of three species as the main contributors to the surface speciation. Two bidentate species were found with the C-C bond parallel to the TiO(2) surface, one monoprotonated and one deprotonated, and a third species being monodentate and monoprotonated.     

Preparation and properties of inhalable nanocomposite particles: effects of the size, weight ratio of the primary nanoparticles in nanocomposite particles and temperature at a spray-dryer inlet upon properties of nanocomposite particles

Nanoparticles are expected to be applicable to inhalation as carrier but there exist disadvantages because of their size. Their deposition dose to the lung will be small. To overcome this problem and utilize nanoparticles for inhalation, we have prepared nanocomposite particles as drug carriers targeting lungs. The nanocomposite particles are prepared as drug-loaded nanoparticles–additive complex to reach deep in the lungs and to be decomposed into nanoparticles when they deposit into lung. In this study, we examined the effect of preparation condition – inlet temperature, size of primary nanoparticles and weight ratio of primary nanoparticles – on the property of nanocomposite particles.

When the size of primary nanoparticles was 400 nm and inlet temperature was 90 °C, only the nanocomposite particles containing between 45 and 55% of primary nanoparticles could be decomposed into nanoparticles in water. On the other hand, when the inlet temperature was 80 °C, nanocomposite particles were decomposed into nanoparticles independent of the weight ratio of primary nanoparticles. Also, the aerodynamic diameter of the nanocomposite particles was between 1.5 and 2.5 μm, independent of the weight ratio of primary nanoparticles.

When the size of primary nanoparticles was 200 nm and inlet temperature was 70 °C, nanocomposite particles were decomposed into nanoparticles independent of the weight ratio of primary nanoparticles. Also, the aerodynamic diameters of them were almost 2.0 μm independent of the weight ratio of primary nanoparticles. When the nanocomposite particles containing nanoparticles with the size of 200 nm are prepared at 80 °C, no decomposition into nanoparticles was observed in water.

Fine particle values, FPF, of the nanocomposite particles were not affected by the weight ratio of primary nanoparticles when they were prepared at optimum inlet temperature.     

Docking, triggering, and biological activity of dynemicin A in DNA: a computational study

The triggering and biological activity of the naturally occurring enediyne dynemicin A (1) was investigated, both inside and outside the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG).d(CCAGTAGTAG), using density functional theory (B3LYP with the 3-21G and 6-31G(d) basis set), BD(T)/cc-pVDZ (Brueckner doubles with a perturbative treatment of triple excitations), and the ONIOM approach. Enediyne 1 is triggered by NADPH in a strongly exothermic reaction (-88 kcal/mol), which involves a number of intermediate steps. Untriggered 1 has a high barrier for the Bergman cyclization (52 kcal/mol) that is lowered after triggering to 16.7 kcal/mol due to an epoxide opening and the accompanying strain relief. The Bergman reaction of triggered 1 is slightly exothermic by 2.8 kcal/mol. The singlet biradical formed in this reaction is kinetically stable (activation enthalpies of 19.5 and 21.8 kcal/mol for retro-Bergman reactions) and is as reactive as para-benzyne. The activity-relevant docking mode is an edge-on insertion into the minor groove, whereas the intercalation between base pairs, although leading to larger binding energies, excludes a triggering of 1 and the development of its biological activity. Therefore, an insertion-intercalation model is developed, which can explain all known experimental observations made for 1. On the basis of the insertion-intercalation model it is explained why large intercalation energies suppress the biological activity of dynemicin and why double-strand scission can be achieved only in a two-step mechanism that involves two enediyne molecules, explaining thus the high ratio of single-strand to double-strand scission observed for 1.     

An ab initio effective potential for two particles in the field of the core: a reduction of (N + 2)-electron problem to two-electron problem

We have used many-body Green function theory and the two-electron Bethe—Salpeter equation to derive an approximate two-electron position space hamiltonian eigenvalue equation for two electrons in the presence of a closed shell core. The resulting effective hamiltonian is nonlocal, energy independent, hermitian and nonadiabatic. It includes all the core—valence, valence—valence exchange effects, core screening effects and electron—electron correlation effects. If a closed form solution of the equation is difficult because of the need to construct the hamiltonian, a semi-empirical approach can be taken which expresses much of the hamiltonian in terms of known properties of the core. A semi-empirical analysis of this effective hamiltonian is shown to give well-known phenomenological effective hamiltonians and the connections to them. Thus this work can also be viewed as a theoretical justification and extension of the two-electron model potential or pseudopotential theories.