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We unambiguously demonstrate the "up" versus "down" alignment of a pair of prototypical solute molecules adsorbed at the air/water interface for the first time using heterodyne-detected electronic sum frequency generation spectroscopy. This molecular alignment is also reproduced by classical molecular dynamics (MD) simulation theoretically. Furthermore, the MD simulation indicates distinctly different interface-specific hydration structures around the two solute molecules, which dictate the molecular alignment at the interface. It is concluded that the hydrophilicity difference between the terminal functional groups of the solute governs the molecular orientation and surrounding hydration structures at the interface.

Microfluidic devices have been developed for imaging behavior and various cellular processes in Caenorhabditis elegans, but not subcellular processes requiring high spatial resolution. In neurons, essential processes such as axonal, dendritic, intraflagellar and other long-distance transport can be studied by acquiring fast time-lapse images of green fluorescent protein (GFP)-tagged moving cargo. We have achieved two important goals in such in vivo studies namely, imaging several transport processes in unanesthetized intact animals and imaging very early developmental stages. We describe a microfluidic device for immobilizing C. elegans and Drosophila larvae that allows imaging without anesthetics or dissection. We observed that for certain neuronal cargoes in C. elegans, anesthetics have significant and sometimes unexpected effects on the flux. Further, imaging the transport of certain cargo in early developmental stages was possible only in the microfluidic device. Using our device we observed an increase in anterograde synaptic vesicle transport during development corresponding with synaptic growth. We also imaged Q neuroblast divisions and mitochondrial transport during early developmental stages of C. elegans and Drosophila, respectively. Our simple microfluidic device offers a useful means to image high-resolution subcellular processes in C. elegans and Drosophila and can be readily adapted to other transparent or translucent organisms., (© 2011 John Wiley & Sons A/S.)

Excited-state proton transfer (ESPT) of pyranine (8-hydroxypyrene-1,3,6-trisulfonate, HPTS) is studied in a polymer-surfactant aggregate using femtosecond emission spectroscopy. The polymer-surfactant aggregate is a supramolecular assembly consisting of a triblock copolymer (PEO)(20)-(PPO)(70)-(PEO)(20) (P123) and a cationic surfactant, cetyltrimethylammonium chloride (CTAC). ESPT of the protonated species (HA) in HPTS leads to the formation of A(-). The dynamics of ESPT may be followed from the decay of the HA emission (at approximately 440 nm) and rise of the A(-) emission (at approximately 550 nm). Both steady-state and time-resolved studies suggest that ESPT of HPTS in P123-CTAC aggregate is much slower than that in bulk water, in P123 micelle, or in CTAC micelle. The ratio of the steady-state emission intensities (HA/A(-)) in P123-CTAC aggregate is 2.2. This ratio is approximately 50, 12, and 2 times higher than that respectively in water, in P123 micelle, and in CTAC micelle. Retardation of ESPT causes an increase in the rise time of the A(-) emission of HPTS. In P123-CTAC aggregate, A(-) displays three rise times: 30, 250, and 2400 ps. These rise times are longer than those in CTAC micelle (23, 250, and 1800 ps), in bulk water (0.3, 3, and 90 ps), and in P123 micelle (15 and 750 ps). The rate constants for initial proton transfer, recombination, and dissociation of the ion pair are estimated using a simple kinetic scheme. The slow fluorescence anisotropy decay of HPTS in P123-CTAC aggregate is analyzed in terms of the wobbling-in-cone model.

DNA amplification using Polymerase Chain Reaction (PCR) in a small volume is used in Lab-on-a-chip systems involving DNA manipulation. For few microliters of volume of liquid, it becomes difficult to measure and monitor the thermal profile accurately and reproducibly, which is an essential requirement for successful amplification. Conventional temperature sensors are either not biocompatible or too large and hence positioned away from the liquid leading to calibration errors. In this work we present a fluorescence based detection technique that is completely biocompatible and measures directly the liquid temperature. PCR is demonstrated in a 3 muL silicon-glass microfabricated device using non-contact induction heating whose temperature is controlled using fluorescence feedback from SYBR green I dye molecules intercalated within sensor DNA. The performance is compared with temperature feedback using a thermocouple sensor. Melting curve followed by gel electrophoresis is used to confirm product specificity after the PCR cycles.

The triblock copolymer (PEO)20-(PPO)70-(PEO)20 (P123) forms a supramolecular aggregate with sodium dodecyl sulfate (SDS). The solvation dynamics and anisotropy decay of coumarin 480 (C480) in different regions of a P123-SDS aggregate are studied through variation of the excitation wavelength (lambdaex) using femtosecond upconversion. In a P123 micelle, because of the drastic differences in polarity between the hydrophilic corona region (PEO block) and the hydrophobic PPO core, C480 exhibits a pronounced red edge excitation shift (REES) of emission maximum by 24 nm. In the P123-SDS aggregate, SDS penetrates the core of the P123 micelle. This increases the polarity of the core and reduces the difference in the polarity between the core and the corona region. In a P123-SDS aggregate, the REES is much smaller (5 nm) which suggests a reduced difference between the core and the corona. Solvation dynamics in a P123 micelle displays a bulklike ultrafast component (<0.3 and 1 ps) in the PEO corona region, a 200 ps component arising from dynamics of polymer segments, and a very long component (5000 or 3000 ps) due to the highly restricted PPO core. In a P123-SDS aggregate, at lambdaex = 375 and 405 nm, the solvation dynamics is found to be faster than that in P123 micelle. In this case, the component (3000 ps) arising from the core region is faster than that (5000 ps) in P123 micelle. In both P123 micelle and P123-SDS aggregate, the relative contribution of the core region decreases and that of the corona region increases with an increase in lambdaex. At lambdaex = 435 nm, which probes the hydrophilic corona, the solvation dynamics for both P123 micelle and P123-SDS aggregate are almost similar.

The primary steps of photoinduced electron transfer (PET) from N,N-dimethylaniline (DMA) to five coumarin dyes are studied in an anionic micelle [sodium dodecyl sulfate (SDS)] and a neutral micelle [triton X-100 (TX-100)] using femtosecond upconversion. The rate of PET in micelle is found to be highly nonexponential. In both the micelles, PET displays components much faster (approximately 10 ps) than the slow components (180-2900 ps) of solvation dynamics. The ultrafast components of electron transfer exhibit a bell-shaped dependence on the free energy change. This is similar to Marcus inversion. The rates of PET in TX-100 and SDS micelle are, in general, faster than those in cetyltrimethylammonium bromide (CTAB) micelle. In the SDS and TX-100 micelle, the Marcus inversion occurs at -DeltaG0 approximately 0.7 eV which is lower than that (approximately 1.2 eV) in CTAB micelle. Possible causes of variation of PET in different micelles are discussed.

Excited-state proton transfer (ESPT) from pyranine (8-hydroxypyrene-1,3,6-trisulfonate, HPTS) to acetate has been studied by picosecond and femtosecond emission spectroscopy in gamma-cyclodextrin (gamma-CD) and 2-hydroxypropyl-gamma-cyclodextrin (HP-gamma-CD) cavities. In both the CDs, ESPT from HPTS to acetate is found to be very much slower (90 and 200 ps) than that in bulk water (0.15 and 6 ps). From molecular modeling, it is shown that in the cyclodextrin cavity the acetate is separated from the OH group of HPTS by water bridges. As a result, proton transfer in the cavity requires rearrangement of the hydrogen-bond network involving the cyclodextrin. This is responsible for the marked slowdown of ESPT. ESPT of HPTS in substituted gamma-CD is found to be slower than that in the unsubstituted one. This is attributed to the hydroxypropyl groups, which prevent close approach of acetate to HPTS.

Photoinduced electron transfer (PET) from N,N-dimethylaniline (DMA) to four coumarin dyes (C151, C481, C153, and C480) inside the cavity of hydroxypropyl gamma-cyclodextrin (hpCD) is studied using femtosecond upconversion. The rate of PET is found to be nonexponential and to vary significantly with the coumarin dyes. The rate for C481 is 100 times faster than that for C480. The PET rate displays a bell-shaped dependence on the free energy change and thus reveals a Marcus-type inverted region. The anisotropy decay of the four dyes in hpCD are found to be very similar, and hence the observed variation in the rate of PET is not due to variation in rotational diffusion of the acceptors (coumarin dyes).

Fluorescence resonance energy transfer (FRET) from coumarin 480 (C480) to fluorescein 548 (F548) in a sodium dioctyl sulfosuccinate (AOT) reverse micelle is studied by picosecond and femtosecond emission spectroscopy. In bulk water, at the low concentration of the donor (C480) and the acceptor (F548), no FRET is observed. However, when the donor (C480) and the acceptor (F548) are confined in a AOT reverse micelle very fast FRET is observed. The time constants of FRET were obtained from the rise time of the emission of the acceptor (F548). In a AOT microemulsion, FRET is found to occur in multiple time scales--3, 200, and 2700 ps. The 3 ps component is assigned to FRET in the water pool of the reverse micelle with a donor-acceptor distance, 16 A. The 200 ps component corresponds to a donor-acceptor distance of 30 A and is ascribed to the negatively charged acceptor inside the water pool and the neutral donor inside the alkyl chains of AOT. The very long 2700 ps component may arise due to FRET from a donor outside the micelle to an acceptor inside the water pool and also from diffusion of the donor from bulk heptane to the reverse micelle. With increase in the excitation wavelength from 375 to 405 nm the relative contribution of the FRET due to C480 in the AOT reverse micelle (the 3 and 200 ps components) increases.

The nature of solvent molecules around proteins in native and different non-native states is crucial for understanding the protein folding problem. We have characterized two compact denatured states of glutaminyl-tRNA synthetase (GlnRS) under equilibrium conditions in the presence of a naturally occurring osmolyte, l-glutamate. The solvation dynamics of the compact denatured states and the fully unfolded state has been studied using a covalently attached probe, acrylodan, near the active site. The solvation dynamics progressively becomes faster as the protein goes from the native to the molten globule to the pre molten globule to the fully unfolded state. Anisotropy decay measurements suggest that the pre-molten-globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that both the compact denatured states are aggregated under the measurement conditions. The implications of solvation dynamics in aggregated compact denatured states have been discussed.

Ultrafast photoinduced electron transfer (PET) from N,N-dimethylaniline to coumarin dyes in cetyltrimethylammonium bromide (CTAB) micelle is studied using femtosecond upconversion spectroscopy. The rate of PET in a CTAB micelle is found to be highly nonexponential with components much faster (approximately 10 ps) than the slow components of solvation dynamics. The ultrafast components of electron transfer exhibits a bell-shaped dependence on the free energy change which is similar to the Marcus inversion.

Ultrafast fluorescence resonance energy transfer (FRET) from coumarin 153 (C153) to rhodamine 6G (R6G) is studied in a neutral PEO(20)-PPO(70)-PEO(20) triblock copolymer (P123) micelle and an anionic micelle (sodium dodecyl sulfate, SDS) using a femtosecond up-conversion setup. Time constants of FRET were determined from the rise time of the acceptor emission. It is shown that a micelle increases efficiency of FRET by holding the donor and the acceptor at a close distance (intramicellar FRET) and also by tuning the donor and acceptor energies. It is demonstrated that in the P123 micelle, intramicellar FRET (i.e., donor and acceptor in same micelle) occurs in 1.2 and 24 ps. In SDS micelle, there are two ultrafast components (0.7 and 13 ps) corresponding to intramicellar FRET. The role of diffusion is found to be minor in the ultrafast components of FRET. We also detected a much longer component (1000 ps) for intramicellar FRET in the larger P123 micelle.

The dependence of fluorescence and solvation dynamics of coumarin 480 (C480) in a dimyristoyl-phosphatidylcholine (DMPC) vesicle on excitation wavelength (lambda(ex)) was studied with femtosecond fluorescence upconversion. The study revealed an ultrafast 1.5-ps component of solvation that was not detected earlier. C480 exhibits pronounced red-edge excitation shift (REES) by 10 nm in a DMPC vesicle. This is due to the microheterogeneity of the lipid vesicle. In lipids, the probe is distributed in different locations with varying static and dynamic electrostatic responses. Solvent relaxation becomes faster and the amount of dynamic Stokes shift decreases with increasing lambda(ex). For excitation at the red end (lambda(ex) = 430 nm), the solvation time was found to be 1.5 ps. However, for excitation at the blue end, (lambda(ex) = 390 nm), there are two substantially slower components of 250 and 2000 ps. It seems that for lambda(ex) = 390 nm, the major contribution to total emission is due to the probe (C480) molecules in the hydrophobic and restricted locations inside the lipid bilayer. Excitation at 430 nm preferentially selects the probe molecules in a highly mobile environment (water pool of the lipid).

Excitation wavelength (lambdaex) dependence of solvation dynamics of coumarin 480 (C480) in the micellar core of a water soluble triblock copolymer, PEO20-PPO70-PEO20 (Pluronic P123), is studied by femtosecond and picosecond time resolved emission spectroscopies. In the P123 micelle, the width of the emission spectrum of C480 is found to be much larger than that in bulk water. This suggests that the P123 micelle is more heterogeneous than bulk water. The steady state emission maximum of C480 in P123 micelle shows a significant red edge excitation shift by 25 nm from 453 nm at lambdaex=345 nm to 478 nm at lambdaex=435 nm. The solvation dynamics in the interior of the triblock copolymer micelle is found to depend strongly on the excitation wavelength. The excitation wavelength dependence is ascribed to a wide distribution of locations of C480 molecules in the P123 micelle with two extreme environments-a bulklike peripheral region with very fast solvent response and a very slow core region. With increase in lambdaex, contribution of the bulklike region having an ultrafast component (< or =2 ps) increases from 7% at lambdaex=375 nm to 78% at lambda(ex)=425 nm while the contribution of the ultraslow component (4500 ps) decreases from 79% to 17%.

Temperature dependence of solvation dynamics and fluorescence anisotropy decay of 8-anilino-1-naphthalenesulfonate (ANS) bound to a protein, bovine serum albumin (BSA), are studied. Solvation dynamics of ANS bound to BSA displays a component (300 ps) which is independent of temperature in the range of 278-318 K and a long component which decreases from 5800 ps at 278 K to 3600 ps at 318 K. The temperature independent part is ascribed to a dynamic exchange of bound to free water with a low barrier. The temperature variation of the long component of solvation dynamics corresponds to an activation energy of 2.1 kcal mol(-1). The activation energy is ascribed to local segmental motion of the protein along with the associated water molecules and polar residues. The time scale of solvation dynamics is found to be very different from the time scale of anisotropy decay. The anisotropy decays are analyzed in terms of the wobbling motion of the probe (ANS) and the overall tumbling of the protein.

Using femtosecond time-resolved fluorescence spectroscopy, it is shown that the solvation dynamics in the two partially folded states (IS' and IS' ') of a protein, cytochrome C, are very different. In the case of IS' (formed by the addition of 2 mM sodium dodecyl sulfate, SDS) almost the entire dynamic solvent shift of coumarin 153 (C153) is captured in a picosecond setup and the contribution of the ultrafast component (0.5 ps) is very small (5%). Solvation dynamics of IS' ' (formed by 2 mM SDS and 5 M urea) displays a major component (47%) of 1.3 ps. This indicates that the structure of IS' ' is much more open and exposed compared to that of IS'. The difference in the dynamics of IS' and IS' ' is attributed to differences in their structure, particularly near the heme region, and the presence of urea in IS' '.

Real time PCR detection systems based on fluorescence detection from intercalating dyes (such as SYBR Green I) typically take only single point measurements during every cycle to quantify the amplification. In this process key information about enzymatic kinetics is lost. In this work we measure SYBR Green I fluorescence intensity every 0.5 s within a cycle during PCR in polypropylene tubes. We observe that the intensity during the extension cycle increases while the template is being extended. Results obtained for different lengths are used to estimate an in vitro polymerase activity rate of Thermus aquaticus and Thermus brockianus. An important practical consequence of this result is that the extension time of each PCR cycle can be individually optimized while the reaction is in progress. We demonstrate this idea of adaptive feedback control and show that the total number of cycles and total time required to reach maximum fluorescence is reduced as compared to conventional PCR.

Fluorescence anisotropy decay and solvation dynamics of coumarin 153 (C153) are studied in dimethyl beta-cyclodextrin (DIMEB) and trimethyl beta-cyclodextrin (TRIMEB) nanocavity in water. C153 binds to DIMEB and TRIMEB to form both 1:1 and 1:2 (C153:cyclodextrin) complexes. The anisotropy decays of C153 in DIMEB and TRIMEB are found to be biexponential. The fast component of anisotropy decay (approximately 1000 ps) is attributed to the 1:1 complex and the slower one (approximately 2500 ps) to the 1:2 complex. From the components of the anisotropy decay, the length of the 1:1 and 1:2 complexes are estimated. Solvation dynamics of C153 in DIMEB exhibits a very fast (2.4 ps) component (41%) and two slower components of 50 ps (29%) and 1450 ps (30%). Solvation dynamics in TRIMEB is described by three slow components of 10.3 ps (24%), 240 ps (45%), and 2450 ps (31%). Possible origins of the ultraslow components are discussed.

Effect of temperature on the fluorescence anisotropy decay and the ultraslow component of solvation dynamics of coumarin 153 (C153) in a gamma-cyclodextrin (gamma-CD) nanocavity are studied using a picosecond set up. The steady-state anisotropy (0.13 +/- 0.01) and residual anisotropy (0.14 +/- 0.01) in fluorescence anisotropy decay in an aqueous solution containing 7 microM C153 and 40 mM gamma-CD are found to be quite large. This indicates formation of large linear nanotube aggregates of gamma-CD linked by C153. It is estimated that >53 gamma-CD units are present in each aggregate. In these aggregates with rise in temperature, the average solvation time ((obs)) decreases markedly from 680 ps at 278 K to 160 ps at 318 K. The dynamic Stokes shift is found to decrease from 800 cm(-1) at 278 K to 250 cm(-1) at 318 K. The fraction of dynamic Stokes shift (f(d)) detected in a picosecond set up is calculated using the Fee-Maroncelli procedure. The corrected solvation time ((corr) = f(d)<(tau(s)>(obs)) displays an Arrhenius type temperature dependence. From the temperature variation, the activation energy and entropy of the solvation process are determined to be 12.5 kcal M(-1) and 28 cal M(-1) K(-1), respectively. The ultraslow component and its temperature dependence are ascribed to a dynamic exchange between bound and free water molecules.

Solvation dynamics at the active site of an enzyme, glutaminyl-tRNA synthetase (GlnRS), was studied using a fluorescence probe, acrylodan, site-specifically attached at cysteine residue C229, near the active site. The picosecond time-dependent fluorescence Stokes shift indicates slow solvation dynamics at the active site of the enzyme, in the absence of any substrate. The solvation dynamics becomes still slower when the substrate (glutamine or tRNA(Gln)) binds to the enzyme. A mutant Y211H-GlnRS was constructed in which the glutamine binding site is disrupted. The mutant Y211H-GlnRS labeled at C229 with acrylodan exhibited significantly different solvent relaxation, thus demonstrating that the slow dynamics is indeed associated with the active site. Implications for catalysis and specificity have been discussed.