Observation of protein folding/unfolding dynamics of ubiquitin trapped in agarose gel by single-molecule FRET.

A ubiquitin mutant with two Cys mutations, m[C]q/S65C, was site-specifically labeled with two dye molecules, Alexa Fluor 488 (donor) and Alexa Fluor 594 (acceptor), due to the different reactivity of these two Cys residues. This doubly dye-labeled ubiquitin has lower structural stability than wild-type ubiquitin. Taking advantage of this decreased stability, conformational heterogeneity of this protein under nondenaturing condition was observed at the single-molecule level using single-paired Förster resonance energy transfer (FRET) by trapping the protein in agarose gel. Three conformational populations corresponding to folded (E (ET) ≈ 0.95), loosely packed (E (ET) ≈ 0.72), and unfolded (E (ET) ≈ 0.22) structures, and the structural transitions between them were observed. Our results suggest that agarose immobilization is good for observing structural dynamics of proteins under native condition.

Studying submicrosecond protein folding kinetics using a photolabile caging strategy and time-resolved photoacoustic calorimetry.

Kinetic measurement of protein folding is limited by the method used to trigger folding. Traditional methods, such as stopped flow, have a long mixing dead time and cannot be used to monitor fast folding processes. Here, we report a compound, 4-(bromomethyl)-6,7-dimethoxycoumarin, that can be used as a "photolabile cage" to study the early stages of protein folding. The folding process of a protein, RD1, including kinetics, enthalpy, and volume change, was studied by the combined use of a phototriggered caging strategy and time-resolved photoacoustic calorimetry. The cage caused unfolding of the photolabile protein, and then a pulse UV laser (∼10(-9) s) was used to break the cage, leaving the protein free to refold and allowing the resolving of two folding events on a nanosecond time scale. This strategy is especially good for monitoring fast folding proteins that cannot be studied by traditional methods.

Synthesis, structure, photoluminescence and photoreactivity of 2,3-diphenyl-4-neopentyl-1-silacyclobut-2-enes.

A series of six 2,3-diphenyl-4-neopentyl-1-silacyclobut-2-enes with different 1,1-substituents has been prepared and characterized by single-crystal X-ray crystallography. These compounds possess a cis-stilbene-like chromophore involving also the four-membered ring, and exhibit a photophysical behavior similar to that of previously reported 1,2-diphenyl-cycloalkenes. This chromophore system is confirmed by a theoretical investigation of the electronic structure and excitation spectra. The absorption and photoluminescence of selected derivatives were studied in solution, as solid powder samples, and in doped-polymer thin films. In well-dissolved solution, the silacyclobutenes show only very weak fluorescence emission (quantum yield approximately 0.1%), due to competition with photochemical and non-radiative photophysical relaxation. When the solubility is degraded in a poor (aqueous) solvent, the formation of nanoscale aggregates leads to a significant enhancement factor in the emission intensity, due to the suppression of the photoreactivity in the more rigid molecular environment, although the quantum yield still remains below a few percent. In the solid-state, however, photoreactivity is completely suppressed leading to fluorescence quantum efficiencies of 8-23% depending on the 1,1-substituents, which demonstrates these compounds' potential as chromophores for condensed-phase luminescence applications. Two dominant competing photochemical reactions have been identified in solution (for excitation in the lowest-energy absorption band, >260 nm), which are analogous to related (sila-)cyclobutenes and stilbenoids. The first involves ring-opening due to cleavage of the 1,4-Si-C bond to form metastable silabutadienes, which was confirmed by isolating the stereospecifically formed allylsilane which results from a secondary reaction with trapping agents such as methanol or water. The second photochemical reaction involves ring closure of the 2,3-diphenyl substructure to form a dihydrophenanthrene analogue, which was confirmed by isolating the phenanthrene derivative that results following subsequent hydrogen abstraction in the presence of oxygen. Measurements of the silacyclobutenes in doped-polymer thin films reveal a spectroscopic behavior ranging from that in solution to the nano-aggregate case as the silacyclobutene dopant concentration is increased.

Coherently aligned porphyrin-appended polynorbornenes.

Six different kinds of coherently aligned porphyrin-appended polynorbornenes derived from 5,6-endo-fused N-arylpyrrolidenonorbornenes have been synthesized. Pi-pi interactions between the pendant groups are essential for dictating the photophysical properties of the polymers and the mechanism for the stereoselective formation of polymers. Splitting of the Soret band of polymers 2a-c, which have alkyl-substituted porphyrin pendant groups, suggests strong exciton coupling between chromophores. No splitting of the Soret band is observed for polymers 2d-f, which have tetraaryl substituents on the porphyrin moiety. Significant fluorescence quenching is found in polymers 2a-e, whereas only slightly reduced quantum yield is observed for 2f. Time-resolved fluorescence measurements also indicate a similar trend. The AFM image of 2d on graphite shows aggregation to form a two-dimensional, ordered pattern.

Fluorescence enhancement and lifetime modification of single nanodiamonds near a nanocrystalline silver surface.

Fluorescent nanodiamond (FND) contains nitrogen-vacancy defect centers as fluorophores. The intensity of its fluorescence can be significantly enhanced after deposition of the particle (35 or 140 nm in size) on a nanocrystalline Ag film without a buffer layer. The excellent photostability (i.e. neither photobleaching nor photoblinking) of the material is preserved even on the Ag film. Concurrent decrease of excited state lifetimes and increase of fluorescence intensities indicate that the enhancement results from surface plasmon resonance. Such a fluorescence enhancement effect is diminished when the individual FND particle is wrapped around by DNA molecules, as a result of an increase in the distance between the color-center emitters inside the FND and the nearby Ag nanoparticles. A fluorescence intensity enhancement up to 10-fold is observed for 35 nm FNDs, confirmed by fluorescence lifetime imaging microscopy.

A new amyloid-like beta-aggregate with amyloid characteristics, except fibril morphology.

Amyloid plaques, formed from amyloid beta (Abeta) peptides (mainly Abeta40 or Abeta42), are one of the most important pathological characteristics of Alzheimer's disease. Here, a single D-form proline substitution in the 40-amino-acid Abeta40 peptide can totally change the aggregation behavior of this peptide. The residue immediately preceding each glycine in Abeta40 (S8, V24, I32, and V36) was individually replaced by D-form proline ((D)Pro). The resulting (D)P-G sequence (the (D)Pro residue and the following Gly residue) was designed as a "structural clip" to force the formation of a bend in the peptide, as this sequence has been reported to be a strong promoter of beta-hairpin formation. The mutant peptide with Val24-to-(D)Pro substitution, named V24P, formed a new amyloid-like beta-aggregate at high peptide concentration. The aggregate has most of the characteristics of amyloid fibrils, except fibril morphology. Moreover, the mutant peptide V24P, when mixed with Abeta40, can attenuate the cytotoxicity of Abeta40.

Mass production and dynamic imaging of fluorescent nanodiamonds.

Fluorescent nanodiamond is a new nanomaterial that possesses several useful properties, including good biocompatibility, excellent photostability and facile surface functionalizability. Moreover, when excited by a laser, defect centres within the nanodiamond emit photons that are capable of penetrating tissue, making them well suited for biological imaging applications. Here, we show that bright fluorescent nanodiamonds can be produced in large quantities by irradiating synthetic diamond nanocrystallites with helium ions. The fluorescence is sufficiently bright and stable to allow three-dimensional tracking of a single particle within the cell by means of either one- or two-photon-excited fluorescence microscopy. The excellent photophysical characteristics are maintained for particles as small as 25 nm, suggesting that fluorescent nanodiamond is an ideal probe for long-term tracking and imaging in vivo, with good temporal and spatial resolution.

Strategy for efficient site-specific FRET-dye labeling of ubiquitin.

To study conformational changes within a single protein molecule, sp-FRET (single pair fluorescence resonance energy transfer) is an important technique to provide distance information. However, incorporating donor and acceptor dyes into the same protein molecule is not an easy task. Here, we report a strategy for the efficient double-labeling of a protein on a solid support. An ubiquitin mutant with two Cys mutations, one with high solvent accessibility and the other with low solvent accessibility, was constructed. The protein was bound to magnetic beads and reacted with the dyes. The first dye reacted with the side-chain of the Cys with the high solvent accessibility and the second with the other Cys under partially denaturing conditions. Using this method, we can easily label two dyes in a site-specific way on ubiquitin with a satisfied yield. The labeling sites for donor and acceptor dyes can be easily swapped.

Combining light harvesting and electron transfer in silica-titania-based organic-inorganic hybrid materials.

A convenient protocol to fabricate an organic-inorganic hybrid system with covalently bound light-harvesting chromophores (stilbene and terphenylene-divinylene) and an electron acceptor (titanium oxide) is described. Efficient energy- and electron-transfer processes may take place in these systems. Covalent bonding between the acceptor chromophores and the titania/silica matrix would be important for electron transfer, whereas fluorescence resonant energy transfer (FRET) would strongly depend on the ratio of donor to acceptor chromophores. Time-resolved spectroscopy was employed to elucidate the detailed photophysical processes. The coupling of FRET and electron transfer was shown to work coherently to lead to photocurrent enhancement. The photocurrent responses reached a maximum when the hybrid-material thin film contained 60 % acceptor and 40 % donor.

Thorpe-Ingold effect on the conformation and photophysical properties of dialkylsilylene-spaced divinylarene copolymers.

Geminal disubstitution on silicon in dialkylsilylene-spaced divinylarene copolymers may dictate the conformation and photophysical properties of the copolymers, bulky (i)Pr substituted copolymers being more folded than Me substituent analogues.

Direct measurements of intersystem crossing rates and triplet decays of luminescent conjugated oligomers in solutions.

Photothermal calorimetry and fluorescence spectroscopy were used to determine the relaxations of the photoexcited singlet state of two PPV and polyfluorene oligomers, (E,E)-1,4-bis[(2-benzyloxy)styryl]benzene (PVDOP) and ter(9,9'-spirobifluorene) (TSBF). The decay rates of different S1 relaxation channels, which include intersystem crossing (ISC), radiative, and nonradiative decay can be determined by the combination of photoacoustic calorimetry (PAC) and the time-correlated single photon counting (TCSPC) technique. The triplet state energy level is determined by the phosphorescence (Ph) spectra recorded at 77 K. The ISC yields are approximately 3% and 6% for PVDOP and TSBF, respectively. The T1 to S0 transition decay rate is acquired by PAC and photothermal beam deflection (PBD) measurements. The triplet state decay rate is 17 and 21 ms(-1) at room temperature. The Ph intensity decay at 77 K shows that the triplet state lifetime increases by 4 orders of magnitude, as compared to room temperature.

Two-photon excited fluorescence of nitrogen-vacancy centers in proton-irradiated type Ib diamond.

Two-photon fluorescence spectroscopy of negatively charged nitrogen-vacancy [(N-V)-] centers in type Ib diamond single crystals have been studied with a picosecond (7.5 ps) mode-locked Nd:YVO(4) laser operating at 1064 nm. The (N-V)- centers were produced by radiation damage of diamond using a 3 MeV proton beam, followed by thermal annealing at 800 degrees C. Prior to the irradiation treatment, infrared spectroscopy of the C-N vibrational modes at 1344 cm(-1) suggested a nitrogen content of 109 +/- 10 ppm. Irradiation and annealing of the specimen led to the emergence of a new absorption band peaking at approximately 560 nm. From a measurement of the integrated absorption intensity of the sharp zero-phonon line (637 nm) at liquid nitrogen temperature, we determined a (N-V)- density of (4.5 +/- 1.1) x 10(18) centers/cm3 (or 25 +/- 6 ppm) for the substrate irradiated at a dose of 1 x 1016) H(+)/cm(2). Such a high defect density allowed us to observe two-photon excited fluorescence and measure the corresponding fluorescence decay time. No significant difference in the spectral feature and fluorescence lifetime was observed between one-photon and two-photon excitations. Assuming that the fluorescence quantum yields are the same for both processes, a two-photon absorption cross section of sigma(TPA) = (0.45 +/- 0.23) x 10(-50) cm(4).s/photon at 1064 nm was determined for the (N-V)- center based on its one-photon absorption cross section of sigma(OPA) = (3.1 +/- 0.8) x 10(-17) cm2 at 532 nm. The material is highly photostable and shows no sign of photobleaching even under continuous two-photon excitation at a peak power density of 3 GW/cm(2) for 5 min.

Characterization and application of single fluorescent nanodiamonds as cellular biomarkers.

Type Ib diamonds emit bright fluorescence at 550-800 nm from nitrogen-vacancy point defects, (N-V)(0) and (N-V)(-), produced by high-energy ion beam irradiation and subsequent thermal annealing. The emission, together with noncytotoxicity and easiness of surface functionalization, makes nano-sized diamonds a promising fluorescent probe for single-particle tracking in heterogeneous environments. We present the result of our characterization and application of single fluorescent nanodiamonds as cellular biomarkers. We found that, under the same excitation conditions, the fluorescence of a single 35-nm diamond is significantly brighter than that of a single dye molecule such as Alexa Fluor 546. The latter photobleached in the range of 10 s at a laser power density of 10(4) W/cm(2), whereas the nanodiamond particle showed no sign of photobleaching even after 5 min of continuous excitation. Furthermore, no fluorescence blinking was detected within a time resolution of 1 ms. The photophysical properties of the particles do not deteriorate even after surface functionalization with carboxyl groups, which form covalent bonding with polyL-lysines that interact with DNA molecules through electrostatic forces. The feasibility of using surface-functionalized fluorescent nanodiamonds as single-particle biomarkers is demonstrated with both fixed and live HeLa cells.

Well-packed chains and aggregates in the emission mechanism of conjugated polymers.

We synthesized dialkoxy-substituted poly[phenylene vinylene]s (dROPPV-1/1, 0.2/1, and 0/1) consisting of two repeating units with different side-chain lengths (methoxy and 3,7-dimethyloctyloxy). These polymers can serve as a model system to clarify roles of aggregates (the sites with ground-state interchain interactions) and the independent chain segments in the well-packed chains (the chain segments that are compactly packed without interaction) in the emission mechanism of conjugated polymers. Due to the packing of polymer chains, films of all of these polymers are accessible to interchain excitations, after which excitons can re-form to result in delayed luminescence. Besides, some chains form aggregates so that the delayed luminescence is no more the ordinary single-chain emission but red-shifted and less structured. Not only the re-formation of these indirect excitons but also the aggregation of chains are facilitated in the polymers with short methoxy side groups, revealing that both packing and aggregation of chain segments require a short spacing between polymer chains. However, the incorporation of other side chains such as the 3,7-dimethyloctyloxy group to dROPPVs is necessary for the formation of aggregates because these long branched side chains can reduce the intrachain order imposed by the short methoxy groups, which accounts for the absence of aggregate emission in the well-studied poly[2,5-dimethoxy-1,4-phenylene vinylene]. This study reveals that the well-packed chains do not necessarily form aggregates. We also show that the photophysical properties and the film morphology of conjugated polymers can be deliberately controlled by fine-tuning of the copolymer compositions, without altering the optical properties of single polymer chains (e.g., as in dilute solutions).

Efficient light harvesting and energy transfer in organic-inorganic hybrid multichromophoric materials.

Thin films of silica hybrid materials consisting of two to three covalently bound organic chromophores at different ratios were conveniently synthesized and fabricated. The photophysical properties of these materials have been studied. The fluorescence spectra reveal complete fluorescence resonance energy transfer (FRET) from donor to acceptor, and the light-harvesting ability of these hybrid materials increases with increasing the molar fraction of donor chromophore. In a three-chromophore system, the energy is transferred from 300 to 530 nm successfully. Time-resolved fluorescence experiments are employed to elucidate the average rates and efficiencies (84-97%) of energy transfer in these organic/inorganic hybrid systems. The hybrid materials have been shown to provide antenna effect to facilitate energy transfer and light harvesting.

Off-angle illumination induced surface plasmon coupling in subwavelength metallic slits.

A directional coupling effect of surface plasmon waves (SPW) in subwavelength metallic slits is studied. The p-polarized wave generates two SPW modes in the subwavelength slit. As the angle of incidence is changed, coupling arises between both SPW modes. The coupling length increases exponentially with the width of the slit but is independent of the angle of incidence. At a coupling length and an incident angle of ~30 degrees , light is emitted from one side of the slit. The single side emission light has a width smaller than 50nm and double peak intensity than at normal incidence. The SPW coupling effect reveals a simple way for producing a nanometer light source of high transmission intensity.

Measuring the refolding of beta-sheets with different turn sequences on a nanosecond time scale.

Whether turns play an active or passive role in protein folding remains a controversial issue at this juncture. Here we use a photolabile cage strategy in combination with laser-flash photolysis and photoacoustic calorimetry to study the effects of different turns on the kinetics of beta-hairpin refolding on a nanosecond time scale. This strategy opens up a temporal window to allow the observation of early kinetic events in the protein refolding process at ambient temperature and pH without interference from any denaturants. Our results provide direct evidence demonstrating that even a one-residue difference in the turn region can change the refolding kinetics of a peptide. This observation suggests an active role for turn formation in directing protein folding.

Optical near field in nanometallic slits.

The propagation and the distribution of the optical near field in nanometallic slits are measured by a near-field scanning optical microscope. The optical near field for the p-polarized wave is confined to the middle of the slit. In contrast, the near field for the s-polarized wave is located at the edges. Asimulation by the finite-difference time-domain method verifies that the near-field distribution for the s-polarized wave is due to the propagation of the surface plasmon wave (SPW) at the air-metal surface. The existence of the SPW also accounts for the extraordinary transmittance of s-polarized light, which is one order of magnitude larger than that of p-polarized light.