6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase

Cyclobutylpyrimidine dimers (CPDs) are formed between adjacent pyrimidines in DNA when it absorbs ultraviolet light. CPDs can be directly repaired by DNA photolyase (PL) in the presence of visible light. How PL recognizes and binds its substrate is still not well understood. Fluorescent nucleic acid base analogues are powerful probes of DNA structure. We have used the fluorescent adenine analogue 6MAP, a pteridone, to probe the local double helical structure of the CPD substrate when bound by photolyase. Duplex melting temperatures were obtained by both UV-vis absorption and fluorescence spectroscopies to ascertain the effect of the probe and the CPD on DNA stability. Steady-state fluorescence measurements of 6MAP-containing single-stranded and doubled-stranded oligos with and without protein show that the local region around the CPD is significantly disrupted. 6MAP shows a different quenching pattern compared to 2-aminopurine, another important adenine analogue, although both probes show that the structure of the complementary strand opposing the 5'-side of the CPD lesion is more destacked than that opposing the 3'-side in substrate/protein complexes. We also show that 6MAP/CPD duplexes are substrates for PL. Vertical excitation energies and transition dipole moment directions for 6MAP were calculated using time-dependent density functional theory. Using these results, the F?rster resonance energy transfer efficiency between the individual adenine analogues and the oxidized flavin cofactor was calculated to account for the observed intensity pattern. These calculations suggest that energy transfer is highly efficient for the 6MAP probe and less so for the 2Ap probe. However, no experimental evidence for this process was observed in the steady-state emission spectra.     

Quadracyclic adenine: a non-perturbing fluorescent adenine analogue

Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300?nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8?% with an emission maximum at 456?nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.     

Suggestion for a new two-photon cross section

We suggest a new two-photon (TP) absorption cross section which is independent of the wavelength of the two laser beams. The different wavelengths may cause changes in the regular cross section by orders of magnitude in the same absorbing molecule. This effect is not due to the resonance term, but to the number of modes.     

The two-photon excitation spectrum of fluorene near 6 K

The two-photon fluorescence excitation spectrum of the fluorene single crystal at about 6 K is reported. Two k = 0 exciton bands arising from the p     

A two-photon absorption cross section measurement in nitric oxide

We report here the measurement of a two-photon absorption cross section for the R₂₂ + S₁₂ (J″ = 9.5) [A ²Σ⁺ (ν′ = 0) - X ²Π (ν′ = 0)] transition in the gamma band system of nitric oxide by measuring the third-order susceptibility using a four-wave mixing technique. A value of σ⁽²⁾ = (1.0 ± 0.6) X 10^?38 πg(2ω₁ ? ω_f) cm⁴ s was obtained.     

The polarised two-photon excitation spectrum of benzene monocrystals at 6 eV

The two-photon excitation spectrum of a benzene single crystal at 4.2 K has been recorded in the region of the second absorption system. The onset of two-photon absorption occurs near 46 500 cm^?1 (quoted as a two-photon frequency). The spectrum has the appearance of a forbidden transition in that the system begins with weak lines which become dominated by an intense continuum at higher energies. The two-photon cross section at 55 000 cm^?1 (the limit reached in this study) is about 200 times greater than at 47 490 cm^?1 although the peak of this strongly allowed system has not yet been reached. The fwhm of the bands near 47 000 cm^?1 is 280 cm^?1, the same as in the one-photon spectrum at these energies. The polarisation ratio is much the same over the entire energy range, and is consistent with the two-photon operators (xz, yz) or (zz). An analysis of all the data available from the one- and two-photon spectra suggests that the transition is ¹B_1u ← ¹A_1g in which the vibronic intensity is derived from the ¹E_1u state in the one-photon and ¹E_1g in the two-photon spectrum.     

Fundamental limits of the dispersion of the two-photon absorption cross section

We rigorously apply the sum rules to the sum-over-states expression to calculate the fundamental limits of the dispersion of the two-photon absorption cross section. A comparison of the theory with the data suggests that the truncated sum rules in the three-level model give a reasonable fundamental limit. Furthermore, we posit that the two-photon absorption cross section near the limit must have only three dominant states, so by default, the three-level model is appropriate. This ansatz is supported by a rigorous analytical calculation that the resonant term gets smaller as more states are added. We also find that the contributions of the nonexplicitly resonant terms cannot be neglected when analyzing real molecules with many excited states, even near resonance. However, puzzling as it may be, extrapolating an off-resonant result to resonance using only the resonant term of the three-level model is shown to be consistent with the exact result. In addition, the off-resonant approximation is shown to scale logarithmically when compared with the full three-level model. This scaling can be used to simplify the analysis of measurements. We find that existing molecules are still far from the fundamental limit; so, there is room for improvement. But, reaching the fundamental limit would require precise control of the energy-level spacing, independently of the transition dipole moments-a task that does not appear possible using today's synthetic approaches. So, we present alternative methods that can still lead to substantial improvements which only require the control of the transition moment to the first excited state. While it is best to normalize measured two-photon absorption cross sections to the fundamental limits when comparing molecules, we show that simply dividing by the square of the number of electrons per molecule yields a good metric for comparison.     

The two-photon excitation spectrum of pyrene

The two-photon excitation spectrum of pyrene and the polarization ratio Ω have been measured up to ≈2100 Å. Evidence of a strong vibronic couplin     

Dicyanostilbene-derived two-photon fluorescence probe for free zinc ions in live cells and tissues with a large two-photon action cross section

A novel two-photon fluorescence probe for Zn(2+) derived from dicyanostilbene as a two-photon fluorophore and 4-(pyridine-2-ylmethyl)piperazine as a novel Zn(2+) ligand was developed. The probe shows a 72.5-fold fluorescence enhancement in response to Zn(2+), a large two-photon action cross-section (580 GM), a noncytotoxic effect, and pH insensitivity in the biologically relevant range, and its dissociation constant (K(d)(TP)) is 0.52 ± 0.01 μM. The probe can selectively detect free Zn(2+) ions in live cells for 1500 s or so and in living tissues at a depth of 80-150 μm without interference from other metal ions and the membrane-bound probes.     

Tracking of mercury ions in living cells with a fluorescent chemodosimeter under single- or two-photon excitation

Tracking of Hg²⁺ in solutions as well as in living cells was conducted with a fluorescent chemodosimeter by measuring the spectral shift of its fluorescence under single- or two-photon excitation. The spectral hypsochromic shifts of this chemodosimeter when reacting with Hg²⁺ were found to be about 50 nm in acetonitrile/water solutions and 32 nm in Euglena gracilis 277 living cells. This chemodosimeter shows high sensitivity and selectivity, and is not influenced by the pH values. It can signal Hg²⁺ in solutions down to the ppb range under either single-photon excitation (SPE) at 405 nm or two-photon excitation (TPE) at 800 nm. However, with low cellular chemodosimeter concentrations, the SPE spectra were disturbed by the auto-fluorescence from the native fluorophore in the cell, while the TPE spectra were still of high quality since the two-photon absorption cross section of this chemodosimeter is much larger than that of the native fluorophores in the cell.     

The two-photon phosphorescence excitation spectrum of triphenylene

The two-proton excited phosphorescence of triphenylene in PMMA matrix at 77 K was measured using a tunable flashlamp-pumped rhodamine dye laser in the effect spectral region 32000–36000 cm^?1. The band origin of the S₀S₂ transition, which is uncertain in the one-photon absorption spectrum, was observed at 33200 cm^?1. The vibronic features in the one-photon spectrum were reinterpreted.     

The two-photon fluorescence excitation spectrum of dibenzothiophene

The two-photon fluorescence excitation spectra of dibenzothiophene crystal (≈77 K) and solution have been investigated in the spectral region 30000–38000 cm^?1 (≈3350-2600 Å). Two electronic transitions have been found. Both the oriented gas model results applied to the crystal and the circular/linear polarization ratio to the solution claim for an ¹A₁ ← ¹A₁ assignment of the transitions. Not completely resolved vibronic structures in the crystal spectrum were observed for both transitions for which a tentative assignment to A₁ total symmetry is discussed. It has been found that the intensity of the first electronic band system arises not only from a purely electronic (i.e., Franck-Condon) mechanism, but also from its interaction with a higher state through totally symmetric vibrations.     

Enlarged pi-electronic network of a meso-meso, beta-beta, beta-beta triply linked dibenzoporphyrin dimer that exhibits a large two-photon absorption cross section

Enlargement of the pi-electronic network of meso-meso, beta-beta, beta-beta triply linked diporphyrin has been exploited by preparing a corresponding dibenzo-fused porphyrin dimer that exhibits a perturbed absorption spectrum and a large two-photon absorption cross section.     

Dye-concentrated organically modified silica nanoparticles as a ratiometric fluorescent pH probe by one- and two-photon excitation

Basic dye-concentrated nanoparticles (approximately 33 nm in diameter) show fluorescence-based ratiometric pH response, by one- and two-photon excitations, with improved proton sensing ability (pKa approximately 6.4) through nanoscopic intraparticle energy transfer.     

Enhancement of two-photon absorption cross section and singlet-oxygen generation in porphyrin-cored star polymers

We report a newly synthesized polymer of a star-shaped porphyrin compound(TPA-FxP) with four oligofluorene arms at its meso positions with the pronounced enhancement of the two-photon properties and the generation of singlet oxygen by utilizing the two-photon excited fluorescence resonance energy transfer.The steady-state spectra and transient triplet-triplet absorption spectra give evidence that the enhanced two-photon absorption cross section results from not only the through-space energy transfer(Frster...     

Properties of a new fluorescent cytosine analogue, pyrrolocytosine

Pyrrolocytosine is a novel, environment sensitive, fluorescent base that can be used in place of cytosine as a fluorescent marker in nucleic acids. In this work the results of a detailed computational investigation into the hybridization and photochemical properties of the base are reported. The interaction energy of the base pair formed between pyrrolocytosine and guanine, calculated at the MP2/6-31G(d,0.25)//HF/6-31G(d,p) level, was found to be -27.2 kcal mol(-1), comparing very favorably with the value calculated for the cytosine and guanine base pair, -25.8 kcal mol(-1). The wavelengths for the vertical transitions of pyrrolocytosine and cytosine were determined using both the configuration interaction technique, with singly excited configurations (CIS) and time-dependent density functional theory using the B3LYP functional (TDB3LYP). It was found that the spacing between the first pipi state and the first npi state was significantly larger in the case of pyrrolocytosine than cytosine, providing a rationale for the higher fluorescence quantum yield of the former. Hydrogen bonding of pyrrolocytosine to guanine did not affect the predicted fluorescence properties of pyrrolocytosine whereas stacking guanine above pyrrolocytosine, in a manner appropriate to B-form DNA, significantly reduced the predicted fluorescence. Calculations on the two base systems using the TDB3LYP method produced low-lying charge-transfer states which are not predicted when the CIS method is used and are not thought to be physically meaningful.