Modulation of pyrene fluorescence in DNA probes depends upon the nature of the conformationally restricted nucleotide

The DNA probes (ODNs) containing a 2'-N-(pyren-1-yl)-group on the conformationally locked nucleosides [2'-N-(pyren-1-yl)carbonyl-azetidine thymidine, Aze-pyr (X), and 2'-N-(pyren-1-yl)carbonyl-aza-ENA thymidine, Aza-ENA-pyr (Y)], show that they can bind to complementary RNA more strongly than to the DNA. The Aze-pyr (X) containing ODNs with the complementary DNA and RNA duplexes showed an increase in the fluorescence intensity (measured at lambda em approximately 376 nm) depending upon the nearest neighbor at the 3'-end to X [dA ( approximately 12-20-fold) > dG ( approximately 9-20-fold) > dT ( approximately 2.5-20-fold) > dC ( approximately 6-13-fold)]. They give high fluorescence quantum yields (Phi F = 0.13-0.89) as compared to those of the single-stranded ODNs. The Aza-ENA-pyr (Y)-modified ODNs, on the other hand, showed an enhancement of the fluorescence intensity only with the complementary DNA (1.4-3.9-fold, Phi F = 0.16-0.47); a very small increase in fluorescence is also observed with the complementary RNA (1.1-1.7-fold, Phi F = 0.17-0.22), depending both upon the site of the Y modification introduced as well as on the chemical nature of the nucleobase adjacent to the modification site into the ODN. The fluorescence properties, thermal denaturation experiments, absorption, and circular dichroism (CD) studies with the X- and Y-modified ODNs in the form of matched homo- and heteroduplexes consistently suggested (i) that the orientation of the pyrene moiety is outside the helix of the nucleic acid duplexes containing a dT-d/rA base pair at the 3'-end of the modification site for both X and Y types of modifications, and (ii) that the microenvironment around the pyrene moiety in the ODN/DNA and ODN/RNA duplexes is dictated by the chemical nature of the conformational constraint in the sugar moiety, as well as by the nature of neighboring nucleobases. The pyrene fluorescence emission in both X and Y types of the conformationally restricted nucleotides is found to be sensitive to a mismatched base present in the target RNA: (i) The X-modified ODN showed a decrease ( approximately 37-fold) in the fluorescence intensity (measured at lambda em approximately 376 nm) upon duplex formation with RNA containing a G nucleobase mismatch (dT-rG pair instead of dT-rA) opposite to the modification site. (ii) In contrast, the Y-modified ODN in the heteroduplex resulted in a approximately 3-fold increase in the fluorescence intensity upon dT-rG mismatch, instead of matched dT-rA pair, in the RNA strand. Our data corroborate that the pyrene moiety is intercalated in the X-modified mismatched ODN/RNA (G mismatch) heteroduplex as compared to that of the Y-modified ODN/RNA (G mismatch) heteroduplex, in which it is located outside the helix.     

Enhanced electrochemical performance of LiNi0.83Co0.12Mn0.05O2 cathodes with a fast-ion conductor Li0.33La0.56TiO3 coating layer

Journal of Solid State Electrochemistry - Ni-rich layered cathode materials LiNixCoyMn(1-x–y)O2 (x ≥ 0.8) suffer from capacity decay due to structural deterioration during...     

Combinatorial Screening of Water/Proton Permeation of Self-Assembled Pillar[5]arene Artificial Water Channel Libraries

Artificial water channels (AWCs) that selectively transport water and reject ions through bilayer membranes have potential to act as synthetic Aquaporins (AQPs). AWCs can have a similar osmotic permeability, better stability, with simpler manufacture on a larger-scale and have higher functional density and surface permeability when inserted into the membrane. Here, we report the screening of combinatorial libraries of symmetrical and unsymmetrical rim-functionalized PAs A – D that are able to transport ca. 10⁷–10⁸ water molecules/s/channel, which is within 1 order of magnitude of AQPs’ and show total ion and proton rejection. Among the four channels, C and D are 3–4 times more water permeable than A and B when inserted in bilayer membranes. The binary combinations of A – D with different molar ratios could be expressed as an independent (linear ABA ), a recessive (inhibition AB , AC , DB , ACA ), or a dominant (amplification, DBD ) behavior of the water net permeation events.     

Multigram Synthesis of α- and γ-((Hetera)cyclo)alkylpyridines through α-Arylation of (Hetero)aliphatic Nitriles

A systematic study on the S_nAr reaction of halogenated fluoropyridines and (hetero)aliphatic nitrile anions as an approach to the synthesis of functionalized pyridines bearing a (cyclo)alkyl or saturated heterocyclic substituent by is described. The scope of the method was demonstrated on a wide range of (hetero)aliphatic nitriles (including three- to six-membered cycloalkane derivatives and N-, O-, S-containing saturated heterocycles) and all isomeric halogenated 2-and 4-fluoropyridines. High chemo- and regioselectivity (i. e., exclusive substitution of the fluorine atom), as well as excellent scalability of the proposed reaction sequence were demonstrated (up to 450 g for the arylation step or up to 77 g of cycloalkylpyridine over two steps in a single run). The utility of the synthesized products was illustrated in the additional functional group transformations resulting in synthetically valuable pyridine-containing building blocks.     

Delivering Structural Information on the Polar Face of Membrane‐Active Peptides: 19F‐NMR Labels with a Cationic Side Chain

Conformationally constrained non‐racemizing trifluoromethyl‐substituted lysine isosteres [(E)‐ and (Z)‐TCBLys] with charged side chains are presented as a new type of ¹⁹F‐NMR labels for peptide studies. Design of the labels, their synthesis, incorporation into peptides and experimental demonstration of their application for solid state NMR studies of membrane‐active peptides are described. A series of fluorine‐labeled analogues of the helical amphipathic antimicrobial peptide PGLa(Nle) was obtained, in which different lysine residues in the original peptide sequence were replaced, one at a time, by either (E)‐ or (Z)‐TCBLys. Antimicrobial activities of the synthesized analogues were practically the same as those of the parent peptide. The structural and orientational parameters of the helical PGLa(Nle) peptide in model bilayers, as determined using the novel labels confirmed and refined the previously known structure. (E)‐ and (Z)‐TCBLys, as a set of cationic ¹⁹F‐NMR labels, were shown to deliver structural information about the charged face of amphipathic peptides by solid state ¹⁹F‐NMR, previously inaccessible by this method.     

Ergodic decomposition of group actions on rooted trees

We prove a general result about the decomposition into ergodic components of group actions on boundaries of spherically homogeneous rooted trees. Namely, we identify the space of ergodic components with the boundary of the orbit tree associated with the action, and show that the canonical system of ergodic invariant probability measures coincides with the system of uniform measures on the boundaries of minimal invariant subtrees of the tree. Special attention is paid to the case of groups generated by finite automata. Few examples, including the lamplighter group, Sushchansky group, and so-called universal group, are considered in order to demonstrate applications of the theorem.     

Steric control of the excited-state intramolecular proton transfer in 3-hydroxyquinolones: steady-state and time-resolved fluorescence study

3-Hydroxyquinolones (3HQs), similarly to their 3-hydroxychromone analogs, undergo excited state intramolecular proton transfer (ESIPT) resulting in dual emission. In the ground state, 2-phenyl-3HQ derivatives are not flat due to a steric hindrance between the 2-phenyl group and the 3-OH group that participates in the ESIPT reaction. To study the effect of this steric hindrance on the ESIPT reaction, a number of 3HQ derivatives have been synthesized and characterized in different organic solvents by steady-state and time-resolved fluorescence techniques. According to our results, 2-phenyl-3HQ derivatives undergo much faster ESIPT (by nearly 1 order of magnitude) than their 2-methyl-3HQ analogs. Moreover, 1-methyl-2-phenyl-3HQ having a strongly twisted 2-phenyl group undergoes a two- to three-fold slower ESIPT compared to 2-phenyl-3HQ. These results suggest that the flatter conformation of 2-phenyl-3HQ, which allows a close proximity of the 2-phenyl and 3-OH groups, favors a fast ESIPT reaction. The absorption and fluorescence spectra of the 3HQ derivatives additionally confirm that the steric rather than the electronic effect of the 2-phenyl group is responsible for the faster ESIPT reaction. Based on the spectroscopic studies and quantum chemical calculations, we suggest that the 2-phenyl group decreases the rotational freedom of its proximal 3-OH group in the more planar conformation of 2-phenyl-3HQ. As a result, the conformations of 3HQ, where the 3-OH group orients to form an intramolecular H-bond with the 4-carbonyl group, are favored over those with a disrupted intramolecular H-bond. Therefore, the 2-phenyl group sterically favors the intramolecular H-bond and thus accelerates the ESIPT reaction. This conclusion provides a new understanding of the ESIPT process in 3-hydroxyquinolones and related systems and suggests new possibilities for the design of ESIPT based molecular sensors and switchers.     

Modulation of excited-state intramolecular proton transfer by viscosity in protic media

3-Hydroxyquinolones undergo excited-state intramolecular proton transfer (ESIPT), resulting in a dual emission highly sensitive to H-bonding perturbations. Here, we report on the strong effect of viscosity on the dual emission of 2-(2-thienyl)-3-hydroxyquinolone in protic solvents. An increase in viscosity significantly decreases the formation of the ESIPT product, thus changing dramatically the ratio of the two emission bands. Time-resolved studies suggest the presence of solvated species characterized by decay times close to the solvent relaxation times in viscous media. The intramolecular H bond in this species is probably disrupted by the solvent, and therefore, its ESIPT requires a reorganization of the solvation shell for restoring this intramolecular H bond. Thus, the ESIPT reaction of this dye and its dual emission depend on solvent relaxation rates and, therefore, on viscosity. The present results suggest a new physical principle for the fluorescence ratiometric measurement of local viscosity.