Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)₂(dppz)]²⁺ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm⁻¹ for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied.

Efficient electron transfer requires the complex to be intercalated at a G-C base-pair. Identification of preferred intercalation sites is achieved by TRIR monitoring of the nucleobase vibrations before electron transfer.     

Amperometric urea biosensor based on urease and electropolymerized toluidine blue dye as a pH-sensitive redox probe

The electropolymerized toluidine blue film deposited on the glassy carbon electrode show amperometrically detectable pH sensitivity. This feature of polytoluidine blue (PTOB) film was used for a construction of an amperometric urea biosensor. We have observed a linear shift of the formal redox potential with increasing pH value between 4 and 8 giving the slope of 81 mV(Delta) pH(-1). Polytoluidine blue film has had a significantly increased stability and higher electrochemical activity compared to the adsorbed monomeric dye. The polytoluidine blue urea biosensor has been operating at a working potential of -200 mV vs. SCE. The sensitivity of the biosensor was 980 nA mM(-1) cm(-2). The biosensor showed linearity in concentration range up to 0.8 mM with the detection limit of 0.02 mM (S/N=3).     

Transfection mediated by gemini surfactants: engineered escape from the endosomal compartment

The structure of the lipoplex formed from DNA and the sugar-based cationic gemini surfactant 1, which exhibits excellent transfection efficiency, has been investigated in the pH range 8.8-3.0 utilizing small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-TEM). Uniquely, three well-defined morphologies of the lipoplex were observed upon gradual acidification: a lamellar phase, a condensed lamellar phase, and an inverted hexagonal (H(II)) columnar phase. Using molecular modeling, we link the observed lipoplex morphologies and physical behavior to specific structural features in the individual surfactant, illuminating key factors in future surfactant design, viz., a spacer of six methylene groups, the presence of two nitrogens that can be protonated in the physiological pH range, two unsaturated alkyl tails, and hydrophilic sugar headgroups. Assuming that the mechanism of transfection by synthetic cationic surfactants involves endocytosis, we contend that the efficacy of gemini surfactant 1 as a gene delivery vehicle can be explained by the unprecedented observation of a pH-induced formation of the inverted hexagonal phase of the lipoplex in the endosomal pH range. This change in morphology leads to destabilization of the endosome through fusion of the lipoplex with the endosomal wall, resulting in release of DNA into the cytoplasm.     

NMR detection of intermolecular NH.OP hydrogen bonds between guanidinium protons and bisposphonate moieties in an artificial arginine receptor

Hydrogen bonding plays a major role in the selective recognition of guanidinium groups by receptor molecules. The present NMR investigation provides direct experimental evidence of hydrogen bonds in an artificial arginine receptor complex consisting of alpha-N-benzoylarginine ethyl ester and a bisphosphonate tweezers molecule. trans-Hydrogen bond 2hJHP couplings between the phosphonate moieties and individual guanidinium protons as well as the amide proton have been detected by [1H,31P]-HMBC and [31P,1H]-INEPT experiments. The detected hydrogen bonding network in the investigated artificial arginine receptor shows a symmetrical end-on interaction of the guanidinium moiety, which enables concerted rotations and deviates from the structure proposed for the biological arginine fork.     

The molecular geometries of some cyclic nitramines in the gas phase

The structural parameters of 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), (CH₂NNO₂)₃, 1,3-dinitro-1,3-diazacyclopentane (DDCP), CH₂(CH₂NNO₂)₂, andN-nitropyrrolidine (NP), (CH₂)₄NNO₂, have been determined by electron diffraction.The six-membered ring of RDX has a chair form with axial positions of the nitro groups and close to planar bond geometry of the amine nitrogen atoms. The overallC ₃ symmetry of the molecule is in agreement with the experimental data.The conformation of the five-membered ring in DDCP is a half-chair ofC ₂ symmetry, while that in NP is an envelope ofC _S symmetry. The nitro groups are in equatorial positions in both molecules. The conformations of pyrrolidine and imidazolidine cycles show interesting features.The pyramidal geometry of the amine nitrogen atom bonds flattens in going from pyrrolidine andN-chloropyrrolidine to NP and DDCP and then to RDX and to dimethylnitramine (DMNA), (CH₃)₂NNO₂.     

Rational Krylov methods for fractional diffusion problems on graphs

BIT Numerical Mathematics - In this paper we propose a method to compute the solution to the fractional diffusion equation on directed networks, which can be expressed in terms of the graph...     

Two-point Padé approximants for formal Stieltjes series

We prove that certain two-point Padé approximants occupying the diagonal of the Padé table form monotone sequences of lower and upper bounds uniformly converging to a Stieltjes function. The results can be applied to the theory of inhomogeneous media for the calculation of the bounds on the effective transport coefficients of heterogeneous materials.     

Synthesis and properties of monodisperse oligofluorene-functionalized truxenes: highly fluorescent star-shaped architectures

This paper describes the strategy toward novel monodisperse, well-defined, star-shaped oligofluorenes with a central truxene core and from monofluorene to quaterfluorene arms. Introduction of solubilizing n-hexyl groups at both fluorene and truxene moieties results in highly soluble, intrinsically two-dimensional nanosized macromolecules T1-T4. The radius for the largest oligomer of ca. 3.9 nm represents one of the largest known star-shaped conjugated systems. Cyclic voltammetry experiments reveal reversible or quasi-reversible oxidation and reduction processes (Eox = +0.74 to 0.80 V, Ered = -2.66 to 2.80 eV vs Fc/Fc+), demonstrating excellent electrochemical stability toward both p- and n-doping, while the band gaps of the oligomers are quite high (EgCV = 3.20-3.40 eV). Close band gaps of 3.05-3.29 eV have been estimated from the electron absorption spectra. These star-shaped macromolecules demonstrate good thermal stability (up to 400-420 degrees C) and improved glass transition temperatures with an increase in length of the oligofluorene arms (from Tg = 63 degrees C for T1 to 116 degrees C for T4) and show very efficient blue photoluminescence (lambdaPL = 398-422 nm) in both solution (PhiPL = 70-86%) and solid state (PhiPL = 43-60%). Spectroelectrochemical experiments reveal that compounds T1-T4 are stable electrochromic systems which change their color reversibly from colorless in the neutral state (approximately 340-400 nm) to colored (from red to purple color; approximately 500-600 nm) in the oxidized state.     

Dissolution of gold in the DMSO—RX systems. The concept of a donor-acceptor electron transport system

Summary The liquid phase oxidation of gold in donor-acceptor organic and aqueous-organic media has been studied. The compounds [AuCl(Me₂S)], [AuBr(Me₂S)], [AuBr₃(Me₂S)], [Me₃S][AuBr₄], [Me₃S][AuBr₄(Me₂S)]·H₂O, [Me₃SO]-[AuBr₄]·H₂O, [Me₃S][Au₂Br₇(Me₂S)₂]·3H₂O, [Me₃S]₂-[Au₂Br₈]·2DMSO·H₂O, [Me₂(Bu)SO][AuBr₄]·H₂O and [Me₃S]Br were isolated by dissolution of Au⁰ in DMSO-RX mixtures (R = H or Bu; X = Cl or Br). The products were characterized by elemental analysis and i.r. spectroscopy. The nature of the Au⁰-DMSO-RX systems and the oxidant species are discussed in terms of a newly-developed concept of donor-acceptor electron transport (DAET) systems.     

STUDY OF LUMINESCENT FORMS OF THE URANYL ION

Luminescence spectra and luminescence decay kinetics of uranyl sulphate water and uranyl nitrate acetone solutions of different concentrations have been studied. Similar experiments have been done with uranyl sulphate powder under vacuum. It has been experimentally shown that the hydrolysis of uranyl sulphate in water takes place, and under low salt concentrations (0.1-4.0 times 10^-4 M) a luminescence of a basic form of the photoexcited ion with a tentative structure of UO₂OH⁺* has been observed. The luminescence of the acidic form UO⁺* has been observed under higher salt concentrations (1–4 times 10^-2 M) in water and under any salt concentration in acetone. The acidic form has the characteristic emission spectrum possessing vibrational structure. The luminescence concentrational quenching of both photoexcited uranyl forms and exciplex emission have not been observed. The effect of a number of organic quenchers and molecular oxygen on uranyl luminescence has been studied. There is no luminescence quenching by O₂ up to 2 times 10⁶ Pa (20 atm) pressure. The low effectiveness of energy transfer from the photoexcited uranyl forms has been explained in terms of strong steric screening of 5f-uranium (VI) orbital by oxygen atoms and by external filled up uranium electronic shells.