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The ability to routinely detect fluorescent nucleobase analogues at the single-molecule level would create a wealth of opportunities to study nucleic acids. We report the multiphoton-induced fluorescence and single-molecule detection of a dimethylamine-substituted extended-6-aza-uridine (DMAthaU). We show that DMAthaU can exist in a highly fluorescent form, emitting strongly in the visible region (470-560 nm). Using pulse-shaped broadband Ti:sapphire laser excitation, DMAthaU undergoes two-photon (2P) absorption at low excitation powers, switching to three-photon (3P) absorption at high incident intensity. The assignment of a 3P process is supported by cubic response calculations. Under both 2P and 3P excitation, the single-molecule brightness was over an order of magnitude higher than reported previously for any fluorescent base analogue, which facilitated the first single-molecule detection of an emissive nucleoside with multiphoton excitation.

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]

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.

The use of laser desorption laser photoionization time-of-flight mass spectrometry (L2TOFMS) for directly analyzing polynuclear aromatic hydrocarbons (PAHs) in solid waste matrices was evaluated. The results showed that L2TOFMS is a rapid, highly selective and sensitive method for analyzing PAHs. It will be a useful technique for predicting PAH distributions in soils and other solid environmental matrices.

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.