Explore the vast range of titles available.

. DNA sequences with guanine repeats are able to fold as G-quadruplex (G4) structures. This is an alternative DNA conformation in which four guanines are arranged as a tetrad, the structural unit of G4; two or more stacked tetrads form a G4 structure. The hydrogen bonds characterizing G4 are called Hoogsten bonds but more interactions are involved in the G4 structure stabilization. For example, cations work as G4 stabilizers and their role is not restricted to the structural folding. They coordinate the guanines’ carbonilic oxygens located towards the hydrophobic channel of the G4 inner structure. This feature suggests that the G4 could work as a cation biosensor. Biological media are characterized by the simultaneous presence of K + and Na + exhibiting different affinities and thus promoting different topological arrangements in the folding solution. In this article we explore the possibility of using PS2.M, an 18 base long synthetic oligonucleotide, as a detector of K + at concentrations in the range 0mM to 10mM. Our intent is therefore to study a biosensor that is made of the G4 sequence only, without intervention of other coupled molecules. As with most guanine-rich oligonucleotides, also PS2.M shows different structures depending on the folding conditions. In agreement with the literature data, our results outline the expected behavior and the key role of K + and Na + in promoting the folding, with Na + promoting the antiparallel structure formation of PS2.M, even at high concentrations. On the other hand, if PS2.M is folded in 10mM to 100mM KCl solutions, the parallel conformation sets in becoming more and more relevant as concentration grows. In a complex solution of G4 in the presence of both K + and Na + ions, spectra display the coexistence of parallel, antiparallel and mixed type conformations. Results show that the CD spectra values at this wavelength can be diagrammed as a function of the K + concentration to construct a biosensor calibration curve. In conclusion, given a Na + concentration in the range 50mM to 80mM and K + concentration in the range 0mM to 10mM, the measured CD signal at 263.6nm permits a K + concentration measurement with a resolution of ∼ 1 mM.

The single-stranded synthetic oligonucleotide PS2.M is known to provide a basis for developing sensors since it tends to fold into structures called G-quadruplexes (G4) having characteristic topology and orientation with probabilities that depend on the chemical environment. The presence and concentration of cation species are among the key factors that determine the outcome of such a process. PS2.M and other aptamers have been used in several applications in conjunction with various probes, such as hemin, at the cost of increased technical complexity and applicability limitations. We instead validated the application limits of Circular Dichroic spectroscopy (CD) as only measurement method to assay PS2.M as$${\\hbox {K}}^{+}$$K + sensor in a variety of solutions having different chemical complexity. The tested solutions range from simple$$\\hbox {NaCl}$$NaCl and$$\\hbox {KCl}$$KCl solutions to chemically complex solutions like DMEM—Dulbecco’s Modified Eagle Medium—which is widely used in a biological laboratory. PS2.M was also evaluated in solutions of$${\\hbox {KHCO}}_{3}$$KHCO 3 and D-ribose (K:D-rib), an antioxidant potassium compound, to compare its response to the simple$$\\hbox {KCl}$$KCl solution case. Our findings show that, within specific concentration applicability ranges, CD spectra can estimate the$${\\hbox {K}}^{+}$$K + concentration in the examined water solutions even at high$${\\hbox {Na}}{+}$$Na + concentrations with respect to$${\\hbox {K}}^{+}$$K + and in the presence of antioxidant molecules.

The single-stranded synthetic oligonucleotide PS2.M is known to provide a basis for developing sensors since it tends to fold into structures called G-quadruplexes (G4) having characteristic topology and orientation with probabilities that depend on the chemical environment. The presence and concentration of cation species are among the key factors that determine the outcome of such a process. PS2.M and other aptamers have been used in several applications in conjunction with various probes, such as hemin, at the cost of increased technical complexity and applicability limitations. We instead validated the application limits of Circular Dichroic spectroscopy (CD) as only measurement method to assay PS2.M as K + sensor in a variety of solutions having different chemical complexity. The tested solutions range from simple NaCl and KCl solutions to chemically complex solutions like DMEM—Dulbecco’s Modified Eagle Medium—which is widely used in a biological laboratory. PS2.M was also evaluated in solutions of KHCO 3 and D-ribose (K:D-rib), an antioxidant potassium compound, to compare its response to the simple KCl solution case. Our findings show that, within specific concentration applicability ranges, CD spectra can estimate the K + concentration in the examined water solutions even at high Na + concentrations with respect to K + and in the presence of antioxidant molecules.

The single-stranded synthetic oligonucleotide PS2.M is known to provide a basis for developing sensors since it tends to fold into structures called G-quadruplexes (G4) having characteristic topology and orientation with probabilities that depend on the chemical environment. The presence and concentration of cation species are among the key factors that determine the outcome of such a process. PS2.M and other aptamers have been used in several applications in conjunction with various probes, such as hemin, at the cost of increased technical complexity and applicability limitations. We instead validated the application limits of Circular Dichroic spectroscopy (CD) as only measurement method to assay PS2.M as $${\\hbox {K}}^{+}$$ K+ sensor in a variety of solutions having different chemical complexity. The tested solutions range from simple $$\\hbox {NaCl}$$ NaCl and $$\\hbox {KCl}$$ KCl solutions to chemically complex solutions like DMEM—Dulbecco’s Modified Eagle Medium—which is widely used in a biological laboratory. PS2.M was also evaluated in solutions of $${\\hbox {KHCO}}_{3}$$ KHCO3and D-ribose (K:D-rib), an antioxidant potassium compound, to compare its response to the simple $$\\hbox {KCl}$$ KCl solution case. Our findings show that, within specific concentration applicability ranges, CD spectra can estimate the $${\\hbox {K}}^{+}$$ K+ concentration in the examined water solutions even at high $${\\hbox {Na}}{+}$$ Na+ concentrations with respect to $${\\hbox {K}}^{+}$$ K+and in the presence of antioxidant molecules.

. The Modified Directional Index (MDI) is a form factor of the angular spectrum computed from the 2D Fourier transform of an image marking the prevalence of rectilinear features throughout the picture. We study some properties of the index and we apply it to AFM images of cell cytoskeleton regions featuring patterns of rectilinear nearly parallel actin filaments as in the case of microfilaments grouped in bundles. The analysis of AFM images through MDI calculation quantifies the fiber directionality changes which could be related to fiber damages. This parameter is applied to the images of Hs 578Bst cell line, non-tumoral and not immortalized human epithelial cell line, irradiated with X-rays at doses equivalent to typical radiotherapy treatment fractions. In the reported samples, we could conclude that the damages are mainly born to the membrane and not to the cytoskeleton. It could be interesting to test the parameter also using other kinds of chemical or physical agents.

We present the results of a recently developed approach where the interplay between the itinerant and localized character of electrons in narrow band materials is described by adding on-site correlation effects to a first principle band calculation: the single particle band states are treated as mean field solutions of a multi-orbital Hubbard Hamiltonian and the many-body term associated to localized e-e interaction is described in a configuration-interaction scheme. The method allows to calculate hole and electron spectral functions which can be directly compared with spectroscopical results.

We study electron molecules in realistic vertically coupled quantum dots in a strong magnetic field. Computing the energy spectrum, pair correlation functions, and dynamical form factor as a function of inter-dot coupling via diagonalization of the many-body Hamiltonian, we identify structural transitions between different phases, some of which do not have a classical counterpart. The calculated Raman cross section shows how such phases can be experimentally singled out.

We study coupled semiconductor quantum dots theoretically through a generalized Hubbard approach, where intra- and inter-dot Coulomb Correlation, as well as tunneling effects are described on the basis of realistic electron wavefunctions. We find that the ground-state configuration of vertically-coupled double dots undergoes non-trivial quantum transitions as a function of the inter-dot distance d; at intermediate values of d we predict a new phase that should be observable in the addition spectra and in the magnetization changes.

We study the energy spectra of small three-dimensional (3D) and two-dimensional (2D) semiconductor quantum dots through different theoretical approaches (single-site Hubbard and Hartree-Fock hamiltonians); in the smallest dots we also compare with exact results. We find that purely 2D models often lead to an inadequate description of the Coulomb interaction existing in realistic structures, as a consequence of the overestimated carrier localization. We show that the dimensionality of the dots has a crucial impact on (i) the accuracy of the predicted addition spectra; (ii) the range of validity of approximate theoretical schemes. When applied to realistic 3D geometries, the latter are found to be much more accurate than in the corresponding 2D cases for a large class of quantum dots; the single-site Hubbard hamiltonian is shown to provide a very effective and accurate scheme to describe quantum dot spectra, leading to good agreement with experiments.

We show that the addition spectra of semiconductor quantum dots in the presence of magnetic field can be studied through a theoretical scheme that allows an accurate and practical treatment of the single particle states and electron-electron interaction up to large numbers of electrons. The calculated addition spectra exhibit the typical structures of Hund-like shell filling, and account for recent experimental findings. A full three dimensional description of Coulomb interaction is found to be essential for predicting the conductance characteristics of few-electron semiconductor structures.