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Fluorescent base analogues (FBAs) are versatile nucleic acid labels that can replace a native nucleobase, while maintaining base pairing and secondary structure. Following the recent demonstration that free FBAs can be detected at the single-molecule level, the next goal is to achieve this level of detection sensitivity in oligonucleotides. Due to the short-wavelength absorption of most FBAs, multiphoton microscopy has emerged as a promising approach to single-molecule detection. We report the multiphoton-induced fluorescence of 5-(5-(4-methoxyphenyl)thiophen-2-yl)-6-aza-uridine (MeOthaU), a polarity-sensitive fluorescent thymidine analogue, as a nucleoside, and in two single-stranded deoxyribo-oligonucleotides, with and without their complementary strands. Ensemble steady-state and time-resolved measurements in dioxane, following one-photon and two-photon excitation, reveals both strongly and weakly emissive species, assigned as rotamers, while in Tris buffer there are additional non-emissive states, which are attributed to tautomeric forms populated in aqueous environments. The two-photon (2P) brightness for MeOthaU is highest as the free nucleoside in dioxane (10 GM) and lowest as the free nucleoside in Tris buffer (0.05 GM). The species-averaged 2P brightness values in DNA are higher for the single strands (0.66 and 0.82 GM for sequence context AXA and AXT, respectively, where X is MeOthaU) than in the duplex (0.31 and 0.25 GM for AXA and AXT, respectively). Using 2P microscopy with pulse-shaped broadband excitation, we were able to detect single- and double-stranded oligos with a molecular brightness of 0.8–0.9 kHz per molecule. This allowed the detection of as few as 7 DNA molecules in the focus, making it the brightest responsive FBA in an oligonucleotide reported to date. [ABSTRACT FROM AUTHOR]

High-pressure single-crystal X-ray diffraction, intermolecular interaction energy calculations, and density functional theory are used to examine the structure and emission properties of the classical organic rotor hexaphenylbenzene (C6Ph6) during hydrostatic compression to 4.14 GPa. Under applied pressure, the inter-phenyl distance in intermolecular dimers with displaced-stacked conformations gradually shortens, indicating the likelihood for hexaphenylbenzene to undergo mechanofluorochromism, while the stability of the crystal is governed by T-shaped intermolecular phenyl dimers. The theoretical band gaps and UV absorption spectra of hexaphenylbenzene at ambient pressure and 1.05 GPa predict an absorption red-shift by about 50 nm, in agreement with shortening of the intermolecular displaced-stacked interactions in the crystal under pressure. Compression of the intermolecular interactions in hexaphenylbenzene prompts a non-centrosymmetric to centrosymmetric phase transition from orthorhombic Pna21 to monoclinic P21/c at 1.05 GPa, as the approximately hexagonally-packed layers of hexaphenylbenzene molecules adopt a perfect hexagonal arrangement. This pressure-stimulated phase transition involving gain of centrosymmetry is an interesting structural phenomenon that is previously unreported in organic crystals. [ABSTRACT FROM AUTHOR]

The effects of excitation wavelength on the optical properties (emission spectrum and quantum yield) of a luminescent solar concentrator (LSC) containing a fluorescent organic dye (Lumogen F Rot 305) are studied. Excitation at wavelengths on the long-wavelength edge of the absorption spectrum of the dye results in redshifted emission, but the quantum yield remains constant at 100%. The origin of this effect and its consequences are discussed. The extent of the long-wavelength tail of the absorption spectrum of the dye is determined and the importance in reabsorption losses is shown. The optical efficiencies and photon transport probabilities of LSCs containing either an organic dye or a rare-earth lanthanide complex are compared using ray-tracing simulations and experiment. The optical efficiency is shown to depend strongly on the Stokes shift of the fluorophore. The lanthanide complex, which has a very large Stokes shift, exhibits a higher optical efficiency than the dye (64% cf. 50%), despite its lower quantum yield (86% cf. 100%). [c] 2010 Optical Society of America OCIS codes: 260.2510, 300.6280, 250.5460, 350.6050.

The study employs several techniques to present a complete analysis of the crystal structures and time-resolved fluorescence of the adenine-specific DNA methyltransferase M. Taql that contains 2-aminopurine flipped into its active site. The analysis reveals and shows that there exists an alternate binding site in the extra-helical target base of the DNA, proving that thymine assists in delivering the target base into the active site.

The decontamination of a range of 'in-use' stainless steel surgical instruments by conventional hospital reprocessing techniques was studied, using scanning electron microscopic (SEM) and energy dispersive X-ray spectroscopic (EDX) analyses, with results obtained when an Ar:[O.sub.2] RF gas-plasma treatment step was added to the cleaning cycle. In some cases, protein contaminants were still retained on instruments subjected to conventional cleaning and sterilization after seven cleaning cycles. No retention of contamination was evident on the surfaces of instruments that were subjected to gas-plasma cleaning. The efficacy of the plasma decontamination is significantly improved by hydration of the tissue residues immediately before exposure to the plasma. The reasons for this are not known, but it is suggested that the production of excited OH radicals and H atoms within the tissue matrix may play some part. Deposition of fluorescently labeled protein from physiological saline solution shows that protein is incorporated into salt crystals formed on stainless steel surfaces. This protein is resistant to plasma etching, but it is shown that water treatment results in improved cleaning. A combination of effects including physical 'cracking' of the salt crystals under vacuum and dissolution of the inorganic matrix, which could possibly be accelerated by dipolar heating of the aqueous phase, may be responsible. Index Terms--Creutzfeldt-Jakob disease (CJD), decontamination, radio frequency (RF) gas-plasma, surgical instruments.

The fluorescence decay characteristics of 2-aminopurine (2AP) and 2-aminopurine riboside (2APr) were investigated as a function of excitation wavelength in aqueous and ethanolic solutions. Global analysis of the decay data showed that 2AP existed as two emitting species, whereas 2APr existed as a single species.

Photophysical studies of chromophoric linkers in metal–organic frameworks (MOFs) are undertaken commonly in the context of sensing applications, in search of readily observable changes of optical properties in response to external stimuli. The advantages of the MOF construct as a platform for investigating fundamental photophysical behaviour have been somewhat overlooked. The linker framework offers a unique environment in which the chromophore is geometrically constrained and its structure can be determined crystallographically, but it exists in spatial isolation, unperturbed by inter‐chromophore interactions. Furthermore, high‐pressure studies enable the photophysical consequences of controlled, incremental changes in local environment or conformation to be observed and correlated with structural data. This approach is demonstrated in the present study of the trans‐azobenzene chromophore, constrained in the form of the 4,4'‐azobenzenedicarboxylate (abdc) linker, in a UiO topology framework. Previously unobserved effects of pressure‐induced solvation and conformational distortion on the lowest energy, nπ* transition are reported, and interpreted the light of crystallographic data. It was found that trans‐azobenzene remains non‐fluorescent (with a quantum yield less than 10−4) despite the prevention of trans‐cis isomerization by the constraining MOF structure. We propose that efficient non‐radiative decay is mediated by the local, pedal‐like twisting of the azo group that is evident as dynamic disorder in the crystal structure. [ABSTRACT FROM AUTHOR]

The fluorescence decay of rigid 2-aminopurine (AP)-labeled duplexes at 77 K are examined in order to investigate the nature of the conformational states that give rise to the heterogeneous decay of AP and the roles of base dynamics in populating these states. The results have shown that the highly stacked geometry that gives rise to the very short decay time of AP-labeled DNA can be attained only through thermal motion of the bases.

The conformational behaviour of tyramine and phenethylamine as well as the number, geometry and electronic structure of stable conformers are described. The conformer dependence of the TDM orientation and the influence of the OH group on these properties are examined.

Investigated here are the aggregation properties of CuPcS4 in aqueous salt solutions using UV-vis spectroscopy and equilibrium statically mechanics. It is shown that the monomer-dimer model (MD) is unable to describe the qualitative behavior of the molar absorption coefficients at CuPcS4 concentrations above 10 (super -4) M and alternative model that takes into account the formation of trimer and all higher aggregates has to be put forward.

Fluorescent nucleobase analogues (FBAs) have many desirable features in comparison to extrinsic fluorescent labels, but they are yet to find application in ultrasensitive detection. Many of the disadvantages of FBAs arise from their short excitation wavelengths (often in the ultraviolet), making two-photon excitation a potentially attractive approach. Pentacyclic adenine (pA) is a recently developed FBA that has an exceptionally high two-photon brightness. We have studied the two-photon-excited fluorescence properties of pA and how they are affected by incorporation in DNA. We find that pA is more photostable under two-photon excitation than via resonant absorption. When incorporated in an oligonucleotide, pA has a high two-photon cross section and emission quantum yield, varying with sequence context, resulting in the highest reported brightness for such a probe. The use of a two-photon microscope with ultrafast excitation and pulse shaping has allowed the detection of pA-containing oligonucleotides in solution with a limit of detection of ∼5 molecules, demonstrating that practical single-molecule detection of FBAs is now within reach. [ABSTRACT FROM AUTHOR]

The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5′-position and each of the natural bases in the 3′-position are examined, together with the analogous 5′-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked. [ABSTRACT FROM AUTHOR]

Nearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe. [ABSTRACT FROM PUBLISHER]

We describe the preparation and optical characterisation of a coronene tetracarboxylate salt (CS) in polyvinyl alcohol (PVA) thin film solutions processed from water, neat or mixed with varying ratios of a europium tris(hexafluoroacetylacetoanto) diaquo complex [Eu(hfac)3(H2O)2]. Neat CS-PVA showed not only well-defined fluorescence peaks but also a long-lived phosphorescence emission, persisting for more than 1 second. Interaction between the CS and EuIII molecules, mediated by means of carboxylate coordination to the EuIII, was attained by simple incorporation into the PVA polymer matrix and resulted in energy transfer from the coronone antenna to the europium centre. Under various blend ratios of CS and the EuIII complex, total photoluminescence quantum yields of typically around 30% were achieved. The straightforward processing of this type of self-assembled chromophore-lanthanide system into a luminescent polymer film offers potential for application to other chromophores, lanthanides and polymers. [ABSTRACT FROM AUTHOR]

In this review, we introduce photonic crystal fibre as a novel optofluidic microdevice that can be employed as both a versatile chemical sensor and a highly efficient microreactor. We demonstrate that it provides an excellent platform in which light and chemical samples can strongly interact for quantitative spectroscopic analysis or photoactivation purposes. The use of photonic crystal fibre in photochemistry and sensing is discussed and recent results on gas and liquid sensing as well as on photochemical and catalytic reactions are reviewed. These developments demonstrate that the tight light confinement, enhanced light-matter interaction and reduced sample volume offered by photonic crystal fibre make it useful in a wide range of chemical applications. [ABSTRACT FROM AUTHOR]

Synthesis and photophysical characterisation of [Ln(hfac)3DPEPO] complexes (with Ln = Eu, Tb, Yb, Nd, Gd) has been carried out to investigate the factors responsible for the variation in total photoluminescence quantum yield within this family of emissive lanthanide complexes. Electronic absorption and emission spectroscopy, in conjunction with DFT calculations of the excited state of the Eu complex, elucidate the role of each ligand in the sensitisation of the lanthanide through the antenna effect. The X-ray crystal structure of [Gd(hfac)3DPEPO] has been determined and shows an 8-coordinate environment around the Gd and a ten-membered chelate ring involving the DPEPO ligand. Total photoluminescence quantum yields were measured to be 6%, 1% and 2% for Ln = Tb, Nd and Yb, respectively, in comparison with around 80% for Ln = Eu. The lower quantum yield for Nd and Yb, compared with Eu, can be attributed to more efficient quenching of the excited Ln state by high-energy oscillations within the ligands, whereas the lower quantum yield for Tb is assigned to a combination of poor energy transfer from the ligand excited state to the Tb and longer radiative lifetime. [ABSTRACT FROM AUTHOR]

The crystal structures of bis(3-fluoro-salicylaldoximato)nickel(II) and bis(3-methoxy-salicylaldoximato)nickel(II) have been determined at room temperature between ambient pressure and approximately 6 GPa. The principal effect of pressure is to reduce intermolecular contact distances. In the fluoro system molecules are stacked, and the Ni⋅⋅⋅Ni distance decreases from 3.19 Å at ambient pressure to 2.82 Å at 5.4 GPa. These data are similar to those observed in bis(dimethylglyoximato)nickel(II) over a similar pressure range, though contrary to that system, and in spite of their structural similarity, the salicyloximato does not become conducting at high pressure. Ni-ligand distances also shorten, on average by 0.017 and 0.011 Å for the fluoro and methoxy complexes, respectively. Bond compression is small if the bond in question is directed towards an interstitial void. A band at 620 nm, which occurs in the visible spectrum of each derivative, can be assigned to a transition to an antibonding molecular orbital based on the metal 3d( x2− y2) orbital. Time-dependent density functional theory calculations show that the energy of this orbital is sensitive to pressure, increasing in energy as the Ni-ligand distances are compressed, and consequently increasing the energy of the transition. The resulting blueshift of the UV-visible band leads to piezochromism, and crystals of both complexes, which are green at ambient pressure, become red at 5 GPa. [ABSTRACT FROM AUTHOR]