Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad

The solution structure of a cyclic oligonucleotide d has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. Under the appropriate experimental conditions, this molecule self-associates, forming a symmetric dimer stabilized by four intermolecular Watson-Crick base pairs. The resulting four-stranded structure consists of two G:C:A:T tetrads, formed by facing the minor groove side of the Watson-Crick base-pairs. Most probably, the association of the base-pairs is stabilized by coordinating a Na(+) cation. This is the first time that this novel G:C:A:T tetrad has been found in an oligonucleotide structure. This observation increases considerably the number of sequences that may adopt a four-stranded architecture. Overall, the three-dimensional structure is similar to those observed previously in other quadruplexes formed by minor groove alignment of Watson-Crick base pairs. This resemblance strongly suggests that we may be observing a general motif for DNA-DNA recognition.     

The structure and dynamics of DNA in the gas phase

The impact of the transfer from water to the vacuum in the duplex DNA has been explored by using long molecular dynamic simulations. In opposition to chemical intuition, it is found that vaporization of DNA, even at high temperatures, does not lead to a total disruption of the double helix. Rather, the DNA duplex preserves gross structural, energetic, and dynamic features of the conformation of the double helix in aqueous solution. Thus, the two strands remain bound, the global structure has a slight helicity, and the total number of DNA-DNA interactions is not dramatically different from that found in solution. The results provide detailed structural and dynamic information useful to complement current mass spectroscopy studies of DNA structures.     

Quantum state reduction and conditional time evolution of wave-particle correlations in cavity QED

We report measurements in cavity QED of a wave-particle correlation function which records the conditional time evolution of the field of a fraction of a photon. Detection of a photon prepares a state of well-defined phase that evolves back to equilibrium via a damped vacuum Rabi oscillation. We record the regression of the field amplitude. The recorded correlation function is nonclassical and provides an efficiency independent path to the spectrum of squeezing. Nonclassicality is observed even when the intensity fluctuations are classical.     

Pharmacophore Modeling and 3D-QSAR Study of Indole and Isatin Derivatives as Antiamyloidogenic Agents Targeting Alzheimer’s Disease

Thirty-six novel indole-containing compounds, mainly 3-(2-phenylhydrazono) isatins and structurally related 1H-indole-3-carbaldehyde derivatives, were synthesized and assayed as inhibitors of beta amyloid (Aβ) aggregation, a hallmark of pathophysiology of Alzheimer’s disease. The newly synthesized molecules spanned their IC₅₀ values from sub- to two-digit micromolar range, bearing further information into structure-activity relationships. Some of the new compounds showed interesting multitarget activity, by inhibiting monoamine oxidases A and B. A cell-based assay in tau overexpressing bacterial cells disclosed a promising additional activity of some derivatives against tau aggregation. The accumulated data of either about ninety published and thirty-six newly synthesized molecules were used to generate a pharmacophore hypothesis of antiamyloidogenic activity exerted in a wide range of potencies, satisfactorily discriminating the ‘active’ compounds from the ‘inactive’ (poorly active) ones. An atom-based 3D-QSAR model was also derived for about 80% of ‘active’ compounds, i.e., those achieving finite IC₅₀ values lower than 100 μM. The 3D-QSAR model (encompassing 4 PLS factors), featuring acceptable predictive statistics either in the training set (n = 45, q² = 0.596) and in the external test set (n = 14, r²_ext = 0.695), usefully complemented the pharmacophore model by identifying the physicochemical features mainly correlated with the Aβ anti-aggregating potency of the indole and isatin derivatives studied herein.     

Dynamics of B-DNA on the microsecond time scale

We present the first microsecond MD simulation of B-DNA. Trajectory shows good agreement with available data and clarifies the mus dynamics of DNA. The duplex is sampling the B-conformation, but many relevant local transitions are found, including S --> N repuckers (up to 7 N-sugars are found simultaneously), local BII transitions (15% of the dinucleotides are in BII-form; some of these forms are stable for up to 7 ns), and sequence-dependent alpha/gamma transitions (happening in the 7-50 ns time scale, and being stable for up to 80 ns). Partial and total openings are often detected, but no base flipping is found. A.T openings happen after amplification of propeller twist movements, while G.C pairs (which can be opened for up to 1 ns) are opened by a complex mechanism which is often catalyzed by cations. A high affinity Na+ binding site is found in the center of the minor groove. Access to this site by cations is difficult (average entry time 400 ns), but once inside, the ion remains for long periods of time (10-15 ns), producing a sizable narrowing of the minor groove. The essential dynamics of DNA fits well with the pattern of deformation needed to (i) sample uncommon right-handed forms and (ii) sample conformations adopted by DNA when bound to proteins. Clearly, DNA has evolved to be not only a stable structure able to maintain and transmit the genetic information but also a flexible entity whose intrinsic pattern of deformability matches its functional needs.     

Differential pattern of glycogen accumulation after protein phosphatase 1 glycogen-targeting subunit PPP1R6 overexpression, compared to PPP1R3C and PPP1R3A, in skeletal muscle cells

Background

Insulin is a hormone that regulates blood glucose homeostasis and is a central protein in a medical condition termed insulin injection amyloidosis. It is intimately associated with glycaemia and is vulnerable to glycation by glucose and other highly reactive carbonyls like methylglyoxal, especially in diabetic conditions. Protein glycation is involved in structure and stability changes that impair protein functionality, and is associated with several human diseases, such as diabetes and neurodegenerative diseases like Alzheimer's disease, Parkinson's disease and Familiar Amyloidotic Polyneuropathy. In the present work, methylglyoxal was investigated for their effects on the structure, stability and fibril formation of insulin.

Results

Methylglyoxal was found to induce the formation of insulin native-like aggregates and reduce protein fibrillation by blocking the formation of the seeding nuclei. Equilibrium-unfolding experiments using chaotropic agents showed that glycated insulin has a small conformational stability and a weaker dependence on denaturant concentration (smaller m-value). Our observations suggest that methylglyoxal modification of insulin leads to a less compact and less stable structure that may be associated to an increased protein dynamics.

Conclusions

We propose that higher dynamics in glycated insulin could prevent the formation of the rigid cross-β core structure found in amyloid fibrils, thereby contributing to the reduction in the ability to form fibrils and to the population of different aggregation pathways like the formation of native-like aggregates.     

Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases

Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.     

Influence of pulsed magnetic fields on the morphology of bone cells in early stages of growth

The effect of electromagnetic fields on living systems has been studied both in vivo and in vitro in a wide range of organisms, cells and tissues. However, the mechanism of action of electromagnetic fields is not yet clearly defined. This paper presents the results of applying a pulsed magnetic field of 70ms width, intensity of 0.65mT at 4Hz in human osteoblasts, during 45min. The magnetic field application was conducted on crops of both 24 and 48h of proliferation. The effect of applying magnetic fields was assessed using parameters such as cell density, protein content, distribution of F-actin fibrils and β-tubulin and integrity of nuclear structure. The results indicate no alteration in either protein synthesis or nuclear structure, or in the number of cells. However, we observed that exposure to these fields induces changes in the distribution of cytoskeletal proteins of osteoblasts.     

Stability and magnetorheological behaviour of magnetic fluids based on ionic liquids

This paper reports the preparation of magnetic fluids consisting of magnetite nanoparticles dispersed in an ionic liquid. Different additives were used in order to stabilize the fluids. Colloidal stability was checked by magnetic sedimentation, centrifugation and direct observation. The results of these tests showed that a true ferrofluid was only obtained when the nanoparticles were coated with a layer of surfactant compatible with the ionic liquid. These experiments also showed that stability could not be reached just by electrostatic repulsion. The conclusions of the stability tests were confirmed by calculations of the interparticle energies of interaction. The rheological behaviour of the magnetic fluids upon magnetic field application was also investigated. The experimental magnetoviscous response was fitted by a microstructural model. The model considered that the fluids consisted of two populations of particles, one with a magnetic core diameter of 9?nm, and another with a larger diameter. Upon field application chain-like structures are supposed to be induced. According to estimations particles of 9?nm are too small to aggregate upon field application. The results of the calculations showed that the intensity of the magnetoviscous response depends on the concentration and size of the large particles, and on the thickness of the surfactant layers.