Sat, 26 Jul 2008 07:53:03 BST CiteULike: samjlord's library [604 articles] http://www.citeulike.org/user/samjlord CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/samjlord/article/3044450 <i>J. Am. Chem. Soc. (19 July 2008)</i><br /><br />Abstract: Two new highly hyperpolarizable chromophores, based on N,N-bis-(4-methoxyphenyl)aryl-amino donors and phenyl-trifluoromethyl-tricyanofuran (CF3-Ph-TCF) acceptor linked together via À-conjugation through 2,5-divinylenethienyl moieties as the bridge, have been designed and synthesized successfully for the first time. The aryl moieties on the donor side of the chromophore molecules were varied as to be thiophene and 1-n-hexylpyrrole. The linear and nonlinear optical (NLO) properties of all compounds were evaluated in addition to recording relevant thermal and electrochemical data. The properties of the two new molecules were comparatively studied. These results are critically analyzed along with two other compounds, reported earlier from our laboratories and our collaborators, that contain (i) aliphatic chain-bearing aniline and (ii) dianisylaniline as donors, keeping the bridge (2,5-divinylenethienyl-), and the acceptor (CF3-Ph-TCF), constant. Trends in theoretically (density functional theory, DFT) predicted, zero-frequency gas-phase hyperpolarizability [²(0;0,0)] values are shown to be consistent with the trends in ²HRS(2É;É,É), as measured by Hyper-Rayleigh Scattering (HRS), when corrected to zero-frequency using the two-level model (TLM) approximation. Similarly, trends in poling efficiency data (r33/Ep) and wavelength dispersion measured by reflection ellipsometry (using a TengMan apparatus) and attenuated total reflection (ATR) are found to fit the TLM and DFT predictions. A 3-fold enhancement in bulk nonlinearity (r33) is realized as the donor subunits are changed from alkylaniline to dianisylaminopyrrole donors. The results of these studies provide insight into the complicated effects on molecular hyperpolarizability of substituting heteroaromatic subunits into the donor group structures. These studies also demonstrate that, when frequency dependence and electric-field-induced ordering behavior are correctly accounted for, ab initio DFT generated ²(0;0,0) is effective as a predictor of changes in r33 behavior based on chromophore structure modification. Thus DFT can provide valuable insight into the electronic structure origin of complex optical phenomena in organic media. Rational Enhancement of Second-Order Nonlinearity: Bis-(4-methoxyphenyl)hetero-aryl-amino Donor-Based Chromophores: Design, Synthesis, and Electrooptic Activity Joshua Davies Arumugasamy Elangovan Philip Sullivan Benjamin Olbricht Denise Bale Todd Ewy Christine Isborn Bruce Eichinger Bruce Robinson Philip Reid Xiaosong Li Larry Dalton doi:10.1021/ja8007424 J. Am. Chem. Soc. (19 July 2008) 2008-07-26T06:01:57-00:00 2008 J. Am. Chem. Soc. dcdhf http://www.citeulike.org/user/samjlord/article/3043827 <i>Organometallics, Vol. 27, No. 10. (26 May 2008), pp. 2172-2175.</i><br /><br />Abstract: The single-molecule fluorescence microscopy imaging of individual palladium(II) complexes is reported and the requisite high-quantum-yield BODIPY fluorophore tags are synthesized and shown to act as spectators when bound to metal complexes. These combined experimental results lay the fundamental groundwork for studying organometallic reaction chemistry at the single-molecule level using fluorophore tags. Toward the Single-Molecule Investigation of Organometallic Reaction Mechanisms: Single-Molecule Imaging of Fluorophore-Tagged Palladium(II) Complexes Stephen Canham Jonathan Bass Oscar Navarro Sung-Gon Lim Neeladri Das Suzanne Blum doi:10.1021/om800228v Organometallics, Vol. 27, No. 10. (26 May 2008), pp. 2172-2175. 2008-07-25T21:39:03-00:00 2008 Organometallics 27 10 2172 2175 chemistry sms http://www.citeulike.org/user/samjlord/article/3043825 <i>Ann NY Acad Sci, Vol. 1130, No. 1. (1 May 2008), pp. 131-137.</i><br /><br />We highlight our recent achievements in the design of fluorescent dyes for the investigation of chemical reactions on the single-molecule level. These fluorophores are tailored to undergo changes in their photophysical properties upon chemical transformations. Three examples are presented: electrophilic aromatic substitution, phosphoester cleavage, and oxidation of double-bonds. Thin-layer chromatography and fluorescence correlation spectroscopy are used to separate and characterize the different reaction products, respectively. We are planning to develop more fluorescent synthons which enable us to perform single-molecule chemistry of various reactions. 10.1196/annals.1430.006 Fluorescent Probes for Chemical Transformations on the Single-Molecule Level Gregor Jung Alexander Schmitt Michaela Jacob Babette Hinkeldey doi:10.1196/annals.1430.006 Ann NY Acad Sci, Vol. 1130, No. 1. (1 May 2008), pp. 131-137. 2008-07-25T21:37:51-00:00 2008 Ann NY Acad Sci 1130 1 131 137 chemistry sms http://www.citeulike.org/user/samjlord/article/3043755 <i>Journal of Applied Physics, Vol. 103, No. 12. (2008)</i> Photoconductivity in organic thin films: From picoseconds to seconds after excitation J Day S Subramanian JE Anthony Z Lu RJ Twieg O Ostroverkhova Journal of Applied Physics, Vol. 103, No. 12. (2008) 2008-07-25T20:19:08-00:00 2008 Journal of Applied Physics 103 12 AIP dcdhf http://www.citeulike.org/user/samjlord/article/3040985 <i>Trans. Faraday Soc., Vol. 35 (1939), pp. 216-219.</i> Quenching of luminescence by oxygen Hans Kautsky doi:10.1039/TF9393500216 Trans. Faraday Soc., Vol. 35 (1939), pp. 216-219. 2008-07-24T18:48:34-00:00 1939 Trans. Faraday Soc. 35 216 219 The Royal Society of Chemistry photobleaching http://www.citeulike.org/user/samjlord/article/3040951 <i>Journal of Physical Chemistry, Vol. 99, No. 36. (1995), pp. 13368-13379.</i><br /><br />no abstract Fluorescence correlation spectroscopy of triplet states in solution: a theoretical and experimental study Jerker Widengren Uelo Mets Rudolf Rigler Journal of Physical Chemistry, Vol. 99, No. 36. (1995), pp. 13368-13379. 2008-07-24T18:26:25-00:00 1995 Journal of Physical Chemistry 99 36 13368 13379 fcs photophysics http://www.citeulike.org/user/samjlord/article/3039308 <i>Methods (14 July 2008)</i><br /><br />In recent years, the development of fast and highly sensitive microscopy has changed the way of thinking of cell biologists: it became more and more important to study the structural origin for cellular function, and industry turned its attention to the improvement of the required instruments. Optical microscopy has now reached a milestone in sensitivity by resolving the signal of a single, fluorescence-labeled biomolecule within a living cell. First steps towards these pioneering studies were set by methods developed in the late eighties for tracking single biomolecules labeled with fluorescent latex spheres or gold-particles. Meanwhile, a time-resolution of milliseconds for imaging weakly fluorescent cellular structures like small organelles, vesicles, or even single molecules is state-of-the-art. The advances in the fields of microscopy brought new cell biological questions into reach. The investigation of a single fluorescent molecule-or simultaneously of an ensemble of individual molecules-provides principally new information, which is generally hidden in ensemble-averaged signals of molecules. In this paper we describe strategies how to make use of single molecule trajectories for deducing information about nanoscopic structures in a live cell context. In particular, we focus our discussion on elucidating the plasma membrane organization by single molecule tracking. A diffusing membrane constituent-e.g. a protein or a lipid-experiences a manifold of interactions on its path: the most rapid interactions represent the driving force for free diffusion; stronger or correlated interactions can be frequently observed as subdiffusive behavior. Correct interpretation of the data has the potential to shine light on this enigmatic organelle, where membrane rafts, protein microdomains, fences and pickets still frolic through the text-book sketches. We summarize available analytical models and point out potential pitfalls, which may result in quantitative or three even qualitative misinterpretations. Single molecule biophysics has developed from a promising into a powerful tool for the life sciences. We describe here a variant-single molecule tracking-in its application to the life cell plasma membrane. Algorithms for localizing the fluorescent biomolecule and determining its trajectory are described. A particular focus is put on data interpretation via the mean square displacement. Potential pitfalls with consequences on data interpretation are quantitatively discussed. Tracking single molecules in the live cell plasma membrane-Do's and Don't's. Stefan Wieser Gerhard Schütz doi:10.1016/j.ymeth.2008.06.010 Methods (14 July 2008) 2008-07-24T11:50:59-00:00 2008 Methods 1046-2023 biophysics membrane trapping http://www.citeulike.org/user/samjlord/article/3037797 <i>Journal of the American Chemical Society, Vol. 58, No. 8. (1936), pp. 1486-1493.</i> Electric Moments of Molecules in Liquids Lars Onsager Journal of the American Chemical Society, Vol. 58, No. 8. (1936), pp. 1486-1493. 2008-07-23T21:21:05-00:00 1936 Journal of the American Chemical Society 58 8 1486 1493 solvatochromism http://www.citeulike.org/user/samjlord/article/3033423 <i>The Journal of Chemical Physics, Vol. 127, No. 5. (2007)</i><br /><br />View this record in Web of Science Solvation dynamics in protein environments: Comparison of fluorescence upconversion measurements of coumarin 153 in monomeric hemeproteins with molecular dynamics simulations Mintu Halder Prasun Mukherjee Sayantan Bose Mark Hargrove Xueyu Song Jacob Petrich The Journal of Chemical Physics, Vol. 127, No. 5. (2007) 2008-07-22T19:01:25-00:00 2007 The Journal of Chemical Physics 127 5 AIP cpjc http://www.citeulike.org/user/samjlord/article/3025115 <i>Biochemistry, Vol. 46, No. 7. (20 February 2007), pp. 1981-1987.</i><br /><br />Abstract: Photolysis of p-azidoacetophenone (1a) or 2,3,5,6-tetrafluoro-p-azidoacetophenone (1b) releases the corresponding singlet nitrenes 2a and 2b. In aqueous solutions singlet nitrenes relax (1.1 ps and 43 ns, respectively) to the lower energy triplet nitrenes 3a and 3b, intermediates which do not react to form cross-links or adducts with typical amino acids and nucleic acids. In a hydrophobic environment singlet nitrene 2a partitions between forming triplet nitrene 3a and an acyl-substituted didehydroazepine 4a, which can be detected by LFP and time-resolved IR spectroscopy. The absolute rate constant of reaction of didehydroazepine 4a with water, in acetonitrile, was determined (3.5 × 104 M-1 s-1) by laser flash photolysis (LFP) techniques with IR detection at ambient temperature. Photolysis of tetrafluoro azide 1b releases singlet nitrene 2b, which has a lifetime of 172 ns in benzene and can readily be intercepted by pyridine to form ylide 10b (max = 415 nm). Singlet nitrene 2b reacts with the unactivated CH bonds of cyclohexane to form adduct 8b in 46% yield. Absolute rate constants of reaction of 1b with N-methylimidazole, phenol, dibutyl sulfide, indole, methanol, and dimethyl sulfoxide were determined using the pyridine ylide probe method. It is concluded that photolysis of p-azidoacetophenone (1a) will not lead to cross-link formation but that tetrafluorinated azide 1b can form useful singlet nitrene derived adducts upon photolysis. Identification of the Reactive Intermediates Produced upon Photolysis of p-Azidoacetophenone and Its Tetrafluoro Analogue in Aqueous and Organic Solvents: Implications for Photoaffinity Labeling MR Cline SM Mandel MS Platz doi:10.1021/bi061269j Biochemistry, Vol. 46, No. 7. (20 February 2007), pp. 1981-1987. 2008-07-21T17:36:53-00:00 2007 Biochemistry 46 7 1981 1987 click-chemistry photochemistry http://www.citeulike.org/user/samjlord/article/3023315 <i>American Journal of Physics, Vol. 76, No. 6. (2008), pp. 551-557.</i><br /><br />The Diet Coke and Mentos reaction is a fun demonstration in chemistry and physics classes of many important concepts in thermodynamics, fluid dynamics, surface science, and the physics of explosions. The reaction has been performed numerous times on television and the Internet, but has not been systematically studied. We report on an experimental study of the Diet Coke and Mentos reaction, and consider many aspects of the reaction, including the ingredients in the candy and soda, the roughness of the candy, the temperature of the soda, and the duration of the reaction. ©2008 American Association of Physics Teachers Diet Coke and Mentos: What is really behind this physical reaction? Tonya Coffey doi:10.1119/1.2888546 American Journal of Physics, Vol. 76, No. 6. (2008), pp. 551-557. 2008-07-21T00:59:34-00:00 2008 American Journal of Physics 76 6 551 557 AAPT fun http://www.citeulike.org/user/samjlord/article/3010669 <i>Chemical Reviews, Vol. 103, No. 10. (2003), pp. 3899-4032.</i><br /><br />no abstract Structural Changes Accompanying Intramolecular Electron Transfer: Focus on Twisted Intramolecular Charge-Transfer States and Structures ZR Grabowski K Rotkiewicz W Rettig Chemical Reviews, Vol. 103, No. 10. (2003), pp. 3899-4032. 2008-07-16T22:34:54-00:00 2003 Chemical Reviews 103 10 3899 4032 review tict http://www.citeulike.org/user/samjlord/article/838625 <i>Science (10 August 2006)</i><br /><br />A method for optically imaging intracellular proteins at nanometer spatial resolution is introduced. Numerous sparse subsets of photoactivatable fluorescent protein molecules are activated, localized (to ~2-25 nm), and then bleached. The aggregate position information from all subsets is then assembled into a superresolution image. The method, termed photoactivated localization microscopy (PALM), is demonstrated in thin sections by imaging specific target proteins in lysosomes and mitochondria, and in fixed, whole cells by imaging vinculin at focal adhesions, actin within a lamellipodium, and the distribution of the retroviral protein Gag at the plasma membrane. Imaging Intracellular Fluorescent Proteins at Nanometer Resolution. Eric Betzig George H Patterson Rachid Sougrat O Wolf Lindwasser Scott Olenych Juan S Bonifacino Michael W Davidson Jennifer Lippincott-Schwartz Harald F Hess doi:10.1126/science.1127344 Science (10 August 2006) 2006-09-11T08:46:47-00:00 2006 Science 1095-9203 super-resolution http://www.citeulike.org/user/samjlord/article/2985651 <i>J. Am. Chem. Soc. (2 July 2008)</i><br /><br />Abstract: We report a tetrazole-based, photoclick chemistry that can be employed to selectively functionalize an alkene genetically encoded in a protein inside E. coli cells. The reaction involved the treatment of E. coli cells with cell-permeable tetrazoles followed by a brief photo irradiation at 302 nm (4 min) and an overnight incubation at 4 °C. This in vivo alkene functionalization procedure was simple, straightforward, and nontoxic to E. coli cells. Additionally, fluorescent adducts were formed, facilitating the monitoring of the reaction in vivo. This reaction should offer a new tool for the study of alkene-containing proteins in living systems. Selective Functionalization of a Genetically Encoded Alkene-Containing Protein via "Photoclick Chemistry" in Bacterial Cells Wenjiao Song Yizhong Wang Jun Qu Qing Lin doi:10.1021/ja803598e J. Am. Chem. Soc. (2 July 2008) 2008-07-10T17:14:56-00:00 2008 J. Am. Chem. Soc. bioconjugation click-chemistry photochemistry http://www.citeulike.org/user/samjlord/article/2985649 <i>Acc. Chem. Res. (1 July 2008)</i><br /><br />Abstract: In biology, ²-barrels, cylindrically rolled-up forms of ²-sheets, are ubiquitous structural motifs within various binding proteins, pores, and enzymes. This biological multifunctionality suggested that synthetic artificial ²-barrels would provide access to many different functions beyond the limitations of peptide chemistry. Unlike the relative ease of formation of synthetic (de novo) ±-helix bundles, the synthesis of artificial ²-barrels remains a challenge. To bypass the folding problems involved, we have employed unfoldable rigid-rod scaffolds as privileged staves (staves are the wood strips that form the sides of macroscopic barrels); the resulting barrel-stave supramolecules exhibit their expected multifunctionality. Several rigid rod ²-barrels that act as receptors, ion channels, pores, catalysts, and sensors have been prepared and studied. The most recent topic of interest concerns the use of artificial ²-barrels as multicomponent sensors (artificial tongues) in complex analyte matrices. For multicomponent sensing, we have designed artificial ²-barrels to form pores that can open and close in response to chemical stimulation within lipid bilayers. With use of fluorogenic vesicles, changes in pore activity are readily detectable with either the naked eye or multiwell screening formats. The varying responsiveness to substrates and products makes synthetic pores versatile detectors of chemical reactions, of the activity of the enzymes that catalyze these reactions, and of their inhibitors. In sensing applications, the perfect selectivity of enzymes is exploited to generate analyte-specific signals. Reactive signal amplifiers are then covalently linked to the products of enzymatic signal generation to enhance their pore blockage potency. With the help of signal generators and amplifiers, we have employed artificial ²-barrel pores to sense sweet (sucrose, lactose), sour (acetate, lactate, citrate), and umami (deliciousness, glutamate) components in various food samples. This breakthrough naturally led us to design and synthesize refined pores for advanced sensing applications. We have developed methods to build guest-binding sites not only at internal and external barrel surfaces but also near the core or near the periphery of the pore. Further refinements include the introduction of asymmetric staves for voltage gating and anchoring of the pore at the membranewater interface. Artificial beta-Barrels Naomi Sakai Jiri Mareda Stefan Matile doi:10.1021/ar700229r Acc. Chem. Res. (1 July 2008) 2008-07-10T17:10:59-00:00 2008 Acc. Chem. Res. gfp http://www.citeulike.org/user/samjlord/article/2982703 <i>J. Am. Chem. Soc. (3 July 2008)</i><br /><br />Abstract: Green fluorescent protein (GFP) has been reassembled from two pieces, a large fragment 214 amino acids in length that is produced recombinantly (GFP 110) and a short synthetic peptide corresponding to the 11th stave of the ²-barrel that is 16 amino acids long (synthetic GFP 11), following a system developed by Waldo and co-workers (Cabantous, S.; et al. Nat. Biotechnol. 2005, 23, 1027) as an in vivo probe for protein association and folding. We demonstrate that the reassembled protein has identical absorption and excited-state proton transfer dynamics as a whole protein of the identical sequence. We show that the reassembled protein can be taken apart and the peptide replaced with a different synthetic peptide designed to perturb the chromophore absorption. Thus, this semisynthetic reassembly process offers a general route for studying the assembly of the ²-barrel as well as the introduction of unnatural amino acids. Deconstructing Green Fluorescent Protein Kevin Kent William Childs Steven Boxer doi:10.1021/ja803782x J. Am. Chem. Soc. (3 July 2008) 2008-07-09T18:05:08-00:00 2008 J. Am. Chem. Soc. bioconjugation gfp http://www.citeulike.org/user/samjlord/article/2961470 <i>Energy, Vol. 31, No. 12. (September 2006), pp. 1685-1702.</i><br /><br />Exergy is used as a common currency to assess and compare the reservoirs of theoretically extractable work we call energy resources. Resources consist of matter or energy with properties different from the predominant conditions in the environment. These differences can be classified as physical, chemical, or nuclear exergy. This paper identifies the primary exergy reservoirs that supply exergy to the biosphere and quantifies the intensive and extensive exergy of their derivative secondary reservoirs, or resources. The interconnecting accumulations and flows among these reservoirs are illustrated to show the path of exergy through the terrestrial system from input to its eventual natural or anthropogenic destruction. The results are intended to assist in evaluation of current resource utilization, help guide fundamental research to enable promising new energy technologies, and provide a basis for comparing the resource potential of future energy options that is independent of technology and cost. Quantifying global exergy resources Weston Hermann doi:10.1016/j.energy.2005.09.006 Energy, Vol. 31, No. 12. (September 2006), pp. 1685-1702. 2008-07-03T22:40:20-00:00 2006 Energy 31 12 1685 1702 energy fun http://www.citeulike.org/user/samjlord/article/2953606 <i>Journal of Photochemistry and Photobiology C: Photochemistry Reviews, Vol. 6, No. 2-3. (October 2005), pp. 168-185.</i><br /><br />The photophysics, photochemistry, photobiology, and structural analysis of furocoumarin derivatives have been reviewed from molecular and interdisciplinary points of view. The molecular aspects have been clear in the photoreaction of furocoumarins since the mid-1900s. Since furocoumarin derivatives absorb UVA light and act as photosensitizers, they have been used as helpful molecular probes and as skin disease drugs. The versatility of these compounds is entirely due to their optical properties. The photoexcited furocoumarins react with biomolecules, especially with pyrimidine bases in DNA, and form mono- and di-adducts. [2 + 2] Photocycloaddition reactions play an important role in the formation of mono- and di-adducts. The degree of photobinding in furocoumarins depends on the types of coumarin compounds, the DNA base sequences, the UVA light doses, excitation wavelengths, temperatures, solvents, and other factors. Consequently, choosing the appropriate conditions can easily control the photoreaction. Furocoumarins have been widely employed for many purposes, and the development of the understanding of their photobiology is still in progress. Molecular aspects of furocoumarin reactions: Photophysics, photochemistry, photobiology, and structural analysis Noriko Kitamura Shigeru Kohtani Ryoichi Nakagaki doi:10.1016/j.jphotochemrev.2005.08.002 Journal of Photochemistry and Photobiology C: Photochemistry Reviews, Vol. 6, No. 2-3. (October 2005), pp. 168-185. 2008-07-02T21:05:58-00:00 2005 Journal of Photochemistry and Photobiology C: Photochemistry Reviews 6 2-3 168 185 fun photochemistry http://www.citeulike.org/user/samjlord/article/2953559 <i>Journal of Emergency Medicine, Vol. 17, No. 2. (4 March 1999), pp. 235-237.</i><br /><br />Phytophotodermatitis is a skin eruption that occurs after contact with photosensitizing compounds in plants and exposure to UV light. There are two common presentations of phytophotodermatitis. Acutely, erythema and vesiculation similar to a severe sunburn are noted. After resolution of the inflammation, the involved skin has marked hyperpigmentation. Many plants have been identified that contain furocoumarins (psoralens), including limes, lemons, and celery. We present a patient with an acute phototoxic eruption and hyperpigmentation after contact with limes during a beach vacation. Phytophotodermatitis: the other "lime" disease Ian Weber Charles Davis David Greeson doi:10.1016/S0736-4679(98)00159-0 Journal of Emergency Medicine, Vol. 17, No. 2. (4 March 1999), pp. 235-237. 2008-07-02T20:55:28-00:00 1999 Journal of Emergency Medicine 17 2 235 237 fun photochemistry http://www.citeulike.org/user/samjlord/article/2938284 <i>Nat Meth, Vol. 5, No. 7. (July 2008), pp. 591-596.</i> Whispering-gallery-mode biosensing: label-free detection down to single molecules Frank Vollmer Stephen Arnold doi:10.1038/nmeth.1221 Nat Meth, Vol. 5, No. 7. (July 2008), pp. 591-596. 2008-06-27T20:53:19-00:00 2008 Nat Meth 5 7 591 596 Nature Publishing Group optics http://www.citeulike.org/user/samjlord/article/2931894 <i>J. Am. Chem. Soc. (26 June 2008)</i><br /><br />Abstract: To explore the real-time dynamic behavior of molecular transporters of the cell-penetrating-peptide (CPP) type on a biological membrane, single fluorescently labeled oligoarginine conjugates were imaged interacting with the plasma membrane of Chinese hamster ovary (CHO) cells. The diffusional motion on the membrane, characterized by single-molecule diffusion coefficient and residence time (ÄR), defined as the time from the initial appearance of a single-molecule spot on the membrane (from the solution) to the time the single molecule disappears from the imaging focal plane, was observed for a fluorophore-labeled octaarginine (a model guanidinium-rich CPP) and compared with the corresponding values observed for a tetraarginine conjugate (negative control), a lipid analogue, and a fluorescently labeled protein conjugate (transferrin-Alexa594) known to enter the cell through endocytosis. Imaging of the oligoarginine conjugates was enabled by the use of a new high-contrast fluorophore in the dicyanomethylenedihydrofuran family, which brightens upon interaction with the membrane at normal oxygen concentrations. Taken as a whole, the motions of the octaarginine conjugate single molecules are highly heterogeneous and cannot be described as Brownian motion with a single diffusion coefficient. The observed behavior is also different from that of lipids, known to penetrate cellular membranes through passive diffusion, conventionally involving lateral diffusion followed by membrane bilayer flip-flop. Furthermore, while the octaarginine conjugate behavior shares some common features with transferrin uptake (endocytotic) processes, the two systems also exhibit dissimilar traits when diffusional motions and residence times of single constructs are compared. Additionally, pretreatment of cells with cytochalasin D, a known actin filament disruptor, produces no significant effect, which further rules out unimodal endocytosis as the mechanism of uptake. Also, the involvement of membrane potential in octaargininemembrane interaction is supported by significant changes in the motion with high [K+] treatment. In sum, this first study of single transporter motion on the membrane of a living cell indicates that the mode by which the octaarginine transporter penetrates the cell membrane appears to either be a multimechanism uptake process or a mechanism different from unimodal passive diffusion or endocytosis. Single-Molecule Motions of Oligoarginine Transporter Conjugates on the Plasma Membrane of Chinese Hamster Ovary Cells HL Lee EA Dubikovskaya H Hwang AN Semyonov H Wang LR Jones RJ Twieg WE Moerner PA Wender doi:10.1021/ja710798b J. Am. Chem. Soc. (26 June 2008) 2008-06-26T18:02:57-00:00 2008 J. Am. Chem. Soc. biophysics dcdhf sms http://www.citeulike.org/user/samjlord/article/2924900 <i>J. Am. Chem. Soc., Vol. 128, No. 28. (19 July 2006), pp. 9028-9029.</i><br /><br />Abstract: We introduce single-molecule spectroelectrochemistry (SMS-EC), a powerful new technique for studying electrochemical kinetics in highly heterogeneous systems. This technique uses fluorescence single-molecule spectroscopy to indirectly measure electrochemical kinetics one molecule at a time, offering for the first time the distribution of key electrochemical variables, such as the half-wave potential, E1/2, not just the ensemble averages. In SMS-EC, the potential of the working electrode of an electrochemical cell is linearly scanned while simultaneously measuring the florescence intensity, Ifl(t), of individual single molecules as a function of time in a wide-field microscope. SMS-EC is used herein to study the oxidation at an indium tin oxide (ITO) electrode of single molecules of the organic conjugated polymer F8BT. The results reveal both excited singlet state and ground state oxidation of F8BT. The latter process occurs over a narrow distribution of single-molecule half-wave potential values, indicating a relatively uniform electrochemical potential at the electrode. Single-Molecule Spectroelectrochemistry (SMS-EC) RE Palacios FRF Fan AJ Bard PF Barbara doi:10.1021/ja062848e J. Am. Chem. Soc., Vol. 128, No. 28. (19 July 2006), pp. 9028-9029. 2008-06-25T02:24:28-00:00 2006 J. Am. Chem. Soc. 128 28 9028 9029 chemiluminescence sms http://www.citeulike.org/user/samjlord/article/2908179 <i>Nature, Vol. 453, No. 7198., pp. 1058-1063.</i> Micro-engineered local field control for high-sensitivity multispectral MRI Gary Zabow Stephen Dodd John Moreland Alan Koretsky doi:10.1038/nature07048 Nature, Vol. 453, No. 7198., pp. 1058-1063. 2008-06-19T16:48:34-00:00 Nature 0028-0836 453 7198 1058 1063 Nature Publishing Group fun http://www.citeulike.org/user/samjlord/article/2923946 <i>J. Am. Chem. Soc. (24 June 2008)</i><br /><br />Abstract: We demonstrate a novel and powerful method to study electrogenerated chemiluminescence (ECL) of single nanoparticles (NPs) (r = 25 15 nm) of a conjugated polymer, F8BT, on an ITO electrode in the presence of a co-reactant, such as tri-n-propylamine (TPrAH) in acetonitrile solution. The results reveal that the maximum formation rate of ECL of individual NPs is achieved after a long build-up time (1040 s after pulse application). The high number of detected ECL photons from individual NPs (1500 photons during 100 s) highlights the potential of this technique as a very sensitive analytical method. Additionally, TPrAH acts as a very efficient protecting agent against irreversible electrochemical processes occurring in F8BT, as found in photoluminescence studies. This protection mechanism probably involves the neutralization of holes at the particle surface via electron transfer by both TPrAH and TPrA radical (TPrA"). Electrogenerated Chemiluminescence of Single Conjugated Polymer Nanoparticles Ya-Lan Chang Rodrigo Palacios Fu-Ren Fan Allen Bard Paul Barbara doi:10.1021/ja803454x J. Am. Chem. Soc. (24 June 2008) 2008-06-24T16:07:18-00:00 2008 J. Am. Chem. Soc. chemiluminescence polymers sms http://www.citeulike.org/user/samjlord/article/2923942 <i>Bioconjugate Chem. (24 June 2008)</i><br /><br />Abstract: We describe the design of an optical switch in the chaperonin GroEL that is opened and closed by its ATP- and cochaperonin GroES-driven conformational changes. The switch, based on a fluorophore and a quencher, is engineered into the single-ring variant of the chaperone, and shows dramatic modulation of its fluorescent intensity in response to the transition of the protein between its allosteric states. It, therefore, forms a sensitive probe for the dynamics of the allosteric transitions of this machine, both in the bulk and in single molecules. Design of an Optical Switch for Studying Conformational Dynamics in Individual Molecules of GroEL Gabriel Frank Yakov Kipnis Elena Smolensky Shirley Daube Amnon Horovitz Gilad Haran doi:10.1021/bc800118j Bioconjugate Chem. (24 June 2008) 2008-06-24T16:01:23-00:00 2008 Bioconjugate Chem. proteins sms http://www.citeulike.org/user/samjlord/article/2923936 <i>Org. Lett. (19 June 2008)</i><br /><br />Abstract: We report the synthesis and the photochromic behavior of a newly designed, photochromic, radical diffusion-inhibited hexaarylbiimidazole (HABI) derivative with markedly improved photochromic performance in coloration and decoloration rates as well as greater optical density in the colored state. The thermal bleaching rate (Ä1/2 = 260 ms at 295 K) is the fastest among the reported ones for HABI derivatives. Photochromism of a Radical Diffusion-Inhibited Hexaarylbiimidazole Derivative with Intense Coloration and Fast Decoloration Performance Kana Fujita Sayaka Hatano Daisuke Kato Jiro Abe doi:10.1021/ol801135g Org. Lett. (19 June 2008) 2008-06-24T15:56:14-00:00 2008 Org. Lett. photoswitchable http://www.citeulike.org/user/samjlord/article/2923865 <i>J. Am. Chem. Soc. (24 June 2008)</i><br /><br />Abstract: We have reengineered a red-emitting dicyanomethylenedihydrofuran pushpull fluorophore so that it is dark until photoactivated with a short burst of low-intensity violet light. Photoactivation of the dark fluorogen leads to conversion of an azide to an amine, which shifts the absorption to long wavelengths. After photoactivation, the fluorophore is bright and photostable enough to be imaged on the single-molecule level in living cells. This proof-of-principle demonstration provides a new class of bright photoactivatable fluorophores, as are needed for super-resolution imaging schemes that require active control of single molecule emission. A Photoactivatable Push-Pull Fluorophore for Single-Molecule Imaging in Live Cells Samuel Lord Nicholas Conley Hsiao-Lu Lee Reichel Samuel Na Liu Robert Twieg WE Moerner doi:10.1021/ja802883k J. Am. Chem. Soc. (24 June 2008) 2008-06-24T15:06:26-00:00 2008 J. Am. Chem. Soc. click-chemistry dcdhf fluorogenic fluorophores photochemistry photoswitchable http://www.citeulike.org/user/samjlord/article/2920184 <i>Journal of Raman Spectroscopy, Vol. 39, No. 7. (2008), pp. 827-831.</i><br /><br />Raman measurements on Gillette foam have been carried out to analyze different phases of water in the system. We have shown that in addition to free water molecules, which drain out with aging of foam, water clusters of only a few water molecules are also present in foam. We have analyzed the rate of drainage with the existing theory available in the literature. The nature of water clusters in Gillette foam has also been obtained from ab initio self-consistent field calculations for [H2O]n clusters. Copyright © 2008 John Wiley & Sons, Ltd. Drainage and water clusters in Gillette foam P Bandyopadhyay AK Ojha TK Barik A Roy doi:10.1002/jrs.1921 Journal of Raman Spectroscopy, Vol. 39, No. 7. (2008), pp. 827-831. 2008-06-24T05:14:26-00:00 2008 Journal of Raman Spectroscopy 39 7 827 831 cpjc http://www.citeulike.org/user/samjlord/article/2919919 <i>Physical Chemistry Chemical Physics (2008)</i><br /><br />A mathematical model has been developed to compute the spectroscopic properties of fluorescence systems with multiple Forster transfer pairs in a homogeneous 3-dimensional matrix. This model is based on Forster energy transfer theory and needs only a limited number of parameters which depend only on the properties of the individual dyes and their pair-wise interactions. Yet, the model allows the accurate prediction on the fluorescence properties of systems comprising mutual Forster transfer between three dyes. The model is compared to an experimental system composed of reverse micelles and water soluble dyes. Although the experimental system might include additional effects that may influence the fluorescence properties (e.g. adsorption to the micelle walls, aggregation of the dyes) the agreement between the mathematical model and the experimental system is reasonably good. Fluorescence properties of systems with multiple Forster transfer pairs Zhong Jiang Werner Goedel doi:10.1039/b717210a Physical Chemistry Chemical Physics (2008) 2008-06-24T00:19:29-00:00 2008 Physical Chemistry Chemical Physics fret http://www.citeulike.org/user/samjlord/article/2919292 <i>J. Am. Chem. Soc. (14 June 2008)</i><br /><br />Abstract: The chromophores of the most widely known fluorescent proteins (FPs) are derivatives of a core p-hydroxybenzylidene-imidazolinon-5-one (HBI) motif, which usually occurs as a phenolate anion. Double bond photoisomerization of the exocyclic bridge of HBI is widely held to be an important internal conversion mechanism for FP chromophores. Herein we describe the ground and excited-state electronic structures and potential energy surfaces of two model chromophores: 4-p-hydroxybenzylidiene-1,2-dimethyl-imidazolin-5-one anion (HBDI), representing green FPs (GFPs), and 2-acetyl-4-hydroxybenylidene-1-methyl-imidazolin-5-one anion (AHBMI), representing kindling FPs (KFPs). These chromophores differ by a single substitution, but we observe qualitative differences in the potential energy surfaces which indicate inversion of bond selection in the photoisomerization reaction. Bond selection is also modulated by whether the reaction proceeds from a Z or an E conformation. These configurations correspond to fluorescent and nonfluorescent states of structurally characterized FPs, including some which can be reversibly switched by specific illumination regimes. We explain the difference in bond selectivity via substituent stabilization effects on a common set of charge-localized chemical structures. Different combinations of these structures give rise to both optically active (planar) and twisted intramolecular charge-transfer (TICT) states of the molecules. We offer a prediction of the gas-phase absorption of AHBMI, which has not yet been measured. We offer a hypothesis to explain the unusual fluorescence of AHBMI in DMF solution, as well as an experimental proposal to test our hypothesis. Bond Selection in the Photoisomerization Reaction of Anionic Green Fluorescent Protein and Kindling Fluorescent Protein Chromophore Models Seth Olsen Sean Smith doi:10.1021/ja078193e J. Am. Chem. Soc. (14 June 2008) 2008-06-23T16:49:34-00:00 2008 J. Am. Chem. Soc. gfp http://www.citeulike.org/user/samjlord/article/2919290 <i>J. Am. Chem. Soc. (14 June 2008)</i><br /><br />Abstract: A successful model for the design of efficient dyes for p-type dye-sensitized solar cells (DSSCs) is presented. As an example, a novel and efficient organic dye containing a triphenylamine chromophore has been synthesized and successfully applied in a p-type DSSC. The highest incident photon-to-current conversion efficiency (IPCE) of 18% in the visible region has been obtained, which is the highest value so far in p-type DSSCs. This is remarkably high, considering that only 600 nm thin NiO mesoporous films were used as p-type DSSC electrodes. Design of an Organic Chromophore for P-Type Dye-Sensitized Solar Cells Peng Qin Hongjun Zhu Tomas Edvinsson Gerrit Boschloo Anders Hagfeldt Licheng Sun doi:10.1021/ja8001474 J. Am. Chem. Soc. (14 June 2008) 2008-06-23T16:48:32-00:00 2008 J. Am. Chem. Soc. solar http://www.citeulike.org/user/samjlord/article/2914654 <i>J. Am. Chem. Soc. (21 June 2008)</i><br /><br />Abstract: The catalytic activity of a series of ruthenium(II) complexes in azidealkyne cycloadditions has been evaluated. The [Cp*RuCl] complexes, such as Cp*RuCl(PPh3)2, Cp*RuCl(COD), and Cp*RuCl(NBD), were among the most effective catalysts. In the presence of catalytic Cp*RuCl(PPh3)2 or Cp*RuCl(COD), primary and secondary azides react with a broad range of terminal alkynes containing a range of functionalities selectively producing 1,5-disubstituted 1,2,3-triazoles; tertiary azides were significantly less reactive. Both complexes also promote the cycloaddition reactions of organic azides with internal alkynes, providing access to fully-substituted 1,2,3-triazoles. The ruthenium-catalyzed azidealkyne cycloaddition (RuAAC) appears to proceed via oxidative coupling of the azide and alkyne reactants to give a six-membered ruthenacycle intermediate, in which the first new carbonnitrogen bond is formed between the more electronegative carbon of the alkyne and the terminal, electrophilic nitrogen of the azide. This step is followed by reductive elimination, which forms the triazole product. DFT calculations support this mechanistic proposal and indicate that the reductive elimination step is rate-determining. Ruthenium-Catalyzed Azide&#x2212;Alkyne Cycloaddition: Scope and Mechanism Brant Boren Sridhar Narayan Lars Rasmussen Li Zhang Haitao Zhao Zhenyang Lin Guochen Jia Valery Fokin doi:10.1021/ja0749993 J. Am. Chem. Soc. (21 June 2008) 2008-06-22T05:14:17-00:00 2008 J. Am. Chem. Soc. click-chemistry http://www.citeulike.org/user/samjlord/article/2911689 <i>Vol. Volume 291 (1998), pp. 63-78.</i> Caged fluorescent probes TJ Mitchison KE Sawin JA Theriot K Gee A Mallavarapu Gerard Marriott Vol. Volume 291 (1998), pp. 63-78. 2008-06-21T01:22:06-00:00 1998 Volume 291 63 78 Academic Press photoswitchable http://www.citeulike.org/user/samjlord/article/2909527 <i>Science, Vol. 320, No. 5883. (20 June 2008), pp. 1593-1594.</i><br /><br />10.1126/science.1154983 ECONOMICS: The MPG Illusion Richard Larrick Jack Soll doi:10.1126/science.1154983 Science, Vol. 320, No. 5883. (20 June 2008), pp. 1593-1594. 2008-06-20T08:01:02-00:00 2008 Science 320 5883 1593 1594 fun http://www.citeulike.org/user/samjlord/article/2910458 <i>Microscopy research and technique (30 May 2008)</i><br /><br />Tackling biological problems often involves the imaging and localization of cellular structures on the nanometer scale. Although optical super-resolution below 100 nm can be readily attained with stimulated emission depletion (STED) and photoswitching microscopy methods, attaining an axial resolution <100 nm with focused light generally required the use of two lenses in a 4Pi configuration or exceptionally bright photochromic fluorophores. Here, we describe a simple technical solution for 3D nanoscopy of fixed samples: biological specimens are fluorescently labeled, embedded in a polymer resin, cut into thin sections, and then imaged via STED microscopy with nanoscale resolution. This approach allows a 3D image reconstruction with a resolution <80 nm in all directions using available state-of-the art STED microscopes. Microsc. Res. Tech., 2008. (c) 2008 Wiley-Liss, Inc. 3D reconstruction of high-resolution STED microscope images. Annedore Punge Silvio O Rizzoli Reinhard Jahn Jan Dominik Wildanger Lars Meyer Andreas Schönle Lars Kastrup Stefan W Hell doi:10.1002/jemt.20602 Microscopy research and technique (30 May 2008) 2008-06-20T12:22:53-00:00 2008 Microscopy research and technique 1059-910X super-resolution http://www.citeulike.org/user/samjlord/article/2909276 <i>Science, Vol. 320, No. 5883. (20 June 2008), pp. 1614-1617.</i><br /><br />Nonlinear optics plays a central role in the advancement of optical science and laser-based technologies. We report on the confinement of the nonlinear interaction of light with matter to a single wave cycle and demonstrate its utility for time-resolved and strong-field science. The electric field of 3.3-femtosecond, 0.72-micron laser pulses with a controlled and measured waveform ionizes atoms near the crests of the central wave cycle, with ionization being virtually switched off outside this interval. Isolated sub-100-attosecond pulses of extreme ultraviolet light (photon energy [~] 80 electron volts), containing [~]0.5 nanojoule of energy, emerge from the interaction with a conversion efficiency of [~]10-6. These tools enable the study of the precision control of electron motion with light fields and electron-electron interactions with a resolution approaching the atomic unit of time ([~]24 attoseconds). 10.1126/science.1157846 Single-Cycle Nonlinear Optics E Goulielmakis M Schultze M Hofstetter VS Yakovlev J Gagnon M Uiberacker AL Aquila EM Gullikson DT Attwood R Kienberger F Krausz U Kleineberg doi:10.1126/science.1157846 Science, Vol. 320, No. 5883. (20 June 2008), pp. 1614-1617. 2008-06-20T01:51:51-00:00 2008 Science 320 5883 1614 1617 fun nlo optics http://www.citeulike.org/user/samjlord/article/2909275 <i>Science, Vol. 320, No. 5882. (13 June 2008), pp. 1478-1482.</i><br /><br />Molecular structure is usually determined by measuring the diffraction pattern the molecule impresses on x-rays or electrons. We used a laser field to extract electrons from the molecule itself, accelerate them, and in some cases force them to recollide with and diffract from the parent ion, all within a fraction of a laser period. Here, we show that the momentum distribution of the extracted electron carries the fingerprint of the highest occupied molecular orbital, whereas the elastically scattered electrons reveal the position of the nuclear components of the molecule. Thus, in one comprehensive technology, the photoelectrons give detailed information about the electronic orbital and the position of the nuclei. 10.1126/science.1157980 Laser-Induced Electron Tunneling and Diffraction M Meckel D Comtois D Zeidler A Staudte D Pavicic HC Bandulet H Pepin JC Kieffer R Dorner DM Villeneuve PB Corkum doi:10.1126/science.1157980 Science, Vol. 320, No. 5882. (13 June 2008), pp. 1478-1482. 2008-06-20T01:51:35-00:00 2008 Science 320 5882 1478 1482 fun http://www.citeulike.org/user/samjlord/article/2903282 <i>J. Am. Chem. Soc., Vol. 130, No. 21. (28 May 2008), pp. 6672-6673.</i><br /><br />Abstract: The fluorescence intensity and lifetime of the 4,42-difluoro-4-bora-5-(p-oxoalkyl)phenyl-3a,4a-diaza-s-indacene (1) show a strong correlation with the viscosity of the medium due to the viscosity-dependent twisting of the 5-phenyl group, which gives access to the dark nonemissive excited state. We propose a sensitive and versatile method for measuring the local microviscosity in biological systems, based on the determination of the fluorescence lifetime of 1. Fluorescence lifetime imaging (FLIM) performed on live cells incubated with 1 demonstrates the distinct intracellular lifetime of the molecular rotor of 1.6 0.2 ns corresponding to the intracellular viscosity of ca. 140 cP. Time-resolved fluorescence anisotropy of 1 in cells confirms insignificant binding of the fluorophore. The viscosity value obtained in the present study is considerably higher than that of water and of cellular cytoplasm. The high viscosity of intracellular compartments is likely to play an important role in vital intracellular processes, including the rate of diffusion of reactive oxygen species, causing programmed cell destruction. Molecular Rotor Measures Viscosity of Live Cells via Fluorescence Lifetime Imaging Marina Kuimova Gokhan Yahioglu James Levitt Klaus Suhling doi:10.1021/ja800570d J. Am. Chem. Soc., Vol. 130, No. 21. (28 May 2008), pp. 6672-6673. 2008-06-17T23:21:18-00:00 2008 J. Am. Chem. Soc. 130 21 6672 6673 flim readout tict http://www.citeulike.org/user/samjlord/article/2902949 <i>J. Am. Chem. Soc., Vol. 129, No. 16. (25 April 2007), pp. 4870-4871.</i><br /><br />Abstract: Dronpa is a photoswitchable protein from the family of green fluorescent proteins (GFPs). Photoswitching involves forward and backward proton transfer between a bright deprotonated form (B) and a dark protonated form (A2). We have used femtosecond transient absorption spectroscopy to determine the kinetics of the first step of the photoconversion from the dark to the bright form, which we have measured as 4 ps. The 2-fold isotope effect on the kinetics of this process shows that excited-state proton transfer (ESPT) is involved in this step. It was also demonstrated that the acid-induced protonated form A1 and the photoconverted protonated form A2 are two distinct spectroscopic species. Ultrafast Excited-State Dynamics of the Photoswitchable Protein Dronpa E Fron C Flors G Schweitzer S Habuchi H Mizuno R Ando FC Deschryver A Miyawaki J Hofkens doi:10.1021/ja069365v J. Am. Chem. Soc., Vol. 129, No. 16. (25 April 2007), pp. 4870-4871. 2008-06-17T18:18:56-00:00 2007 J. Am. Chem. Soc. 129 16 4870 4871 gfp photophysics photoswitchable http://www.citeulike.org/user/samjlord/article/1285412 <i>Chemphyschem, Vol. 6, No. 5. (May 2005), pp. 791-804.</i><br /><br />Under high-excitation irradiance conditions in one- and two-photon induced fluorescence microscopy, the photostability of fluorescent dyes is of crucial importance for the detection sensitivity of single molecules and for the contrast in fluorescence imaging. Herein, we report on the dependence of photobleaching on the excitation conditions, using the dye Rhodamine 6G as a typical example. The different excitation modes investigated include 1) one-photon excitation into the first-excited singlet state in the range of 500 to 528 nm by continuous wave and picosecond-pulsed lasers and 2) two- and one-photon excitation to higher-excited singlet states at 800 and 350 nm, respectively, by femtosecond pulses. Experimental strategies are presented, which allow resolving the photophysics. From single-molecule trajectories and fluorescence correlation spectroscopy, as well as with a simple theoretical model based on steady-state solutions of molecular rate equation analysis, we determined the underlying photobleaching mechanisms and quantified the photokinetic parameters describing the dependence of the fluorescence signal on the excitation irradiance. The comparison with experimental data and an exact theoretical model show that only minor deviations between the different theoretical approaches can be observed for high-pulsed excitation irradiances. It is shown that fluorescence excitation is in all cases limited by photolysis from higher-excited electronic states. In contrast to picosecond-pulsed excitation, this is extremely severe for both one- and two-photon excitation with femtosecond pulses. Furthermore, the photostability of the higher-excited electronic states is strongly influenced by environmental conditions, such as polarity and temperature. Molecular photobleaching kinetics of Rhodamine 6G by one- and two-photon induced confocal fluorescence microscopy. C Eggeling A Volkmer CA Seidel doi:10.1002/cphc.200400509 Chemphyschem, Vol. 6, No. 5. (May 2005), pp. 791-804. 2007-05-09T14:51:03-00:00 2005 Chemphyschem 1439-4235 6 5 791 804 photobleaching photochemistry photophysics http://www.citeulike.org/user/samjlord/article/2899293 <i>Anal. Chem., Vol. 70, No. 13. (1 July 1998), pp. 2651-2659.</i><br /><br />Abstract: The photostability of fluorescent dyes is of crucial importance for the statistical accuracy of single-molecule detection (SMD) and for the image quality of scanning confocal microscopy. Concurrent results for the photostability were obtained by two different experimental techniques. First, the photostabilities of several coumarin and rhodamine derivatives in aqueous solution were obtained by monitoring the steady-state fluorescence decay in a quartz cell. Furthermore, an epi-illuminated microscope, continuous wave (CW) excitation at 514.5 nm, and fluorescence correlation spectroscopy (FCS) with a newly developed theory were used to study the photobleaching characteristics of rhodamines under conditions used for SMD. Depending on the rhodamine structure, the probability of photobleaching, pb, is in the order of 10-6-10-7 for irradiances below 103 W/cm2. However, a considerable increase of pb for irradiances above this level was observed which can only be described by photobleaching reactions from higher excited states (two-step photolysis). In view of these observations, the probability of photobleaching, pb, as well as a closed expression of its dependence on the CW excitation irradiance considering a five-level molecular electronic state model with the possibility of photobleaching from higher excited electronic states, is derived. From this model, optimal conditions for SMD with respect to the number of emitted fluorescence photons and to the signal-to-background ratio are discussed, taking into account both saturation and photobleaching. The additional photobleaching due to two-step photolysis limits the applicable irradiance. Photobleaching of Fluorescent Dyes under Conditions Used for Single-Molecule Detection: Evidence of Two-Step Photolysis C Eggeling J Widengren R Rigler CAM Seidel doi:10.1021/ac980027p Anal. Chem., Vol. 70, No. 13. (1 July 1998), pp. 2651-2659. 2008-06-16T18:12:37-00:00 1998 Anal. Chem. 70 13 2651 2659 photobleaching photochemistry photophysics http://www.citeulike.org/user/samjlord/article/2899292 <i>J. Phys. Chem. A, Vol. 110, No. 9. (9 March 2006), pp. 2979-2995.</i><br /><br />Abstract: Dye photobleaching is a major constraint of fluorescence readout within a range of applications. In this study, we investigated the influence of photobleaching in fluorescence experiments applying multicolor laser as well as Förster resonance energy transfer (FRET) mediated excitation using several red-emitting dyes frequently used in multicolor experiments or as FRET acceptors. The chosen dyes (cyanine 5 (Cy5), MR121, Alexa660, Alexa680, Atto647N, Atto655) have chemically distinct chromophore systems and can be excited at 650 nm. Several fluorescence analysis techniques have been applied to detect photobleaching and to disclose the underlying photophysics, all of which are based on single-molecule detection: (1) fluorescence correlation spectroscopy (FCS) of bulk solutions, (2) fluorescence cross-correlation of single-molecule trajectories, and (3) multiparameter fluorescence detection (MFD) of single-molecule events. The maximum achievable fluorescence signals as well as the survival times of the red dyes were markedly reduced under additional laser irradiation in the range of 500 nm. Particularly at excitation levels at or close to saturation, the 500 nm irradiation effectively induced transitions to higher excited electronic states on already excited dye molecules, leading to a pronounced bleaching reactivity. A theoretical model for the observed laser irradiance dependence of the fluorescence brightness of a Cy5 FRET acceptor dye has been developed introducing the full description of the underlying photophysics. The model takes into account acceptor as well as donor photobleaching from higher excited electronic states, population of triplet states, and energy transfer to both the ground and excited states of the acceptor dye. Also, photoinduced reverse intersystem crossing via higher excited triplet states is included, which was found to be very efficient for Cy5 attached to DNA. Comparing continuous wave (cw) and pulsed donor excitation, a strong enhancement of acceptor photobleaching by a factor of 5 was observed for the latter. Thus, in the case of fluorescence experiments utilizing multicolor pulsed laser excitation, the application of the appropriate timing of synchronized green and red laser pulses in an alternating excitation mode can circumvent excessive photobleaching. Moreover, important new single-molecule analysis diagnosis tools are presented: (1) For the case of excessive acceptor photobleaching, cross-correlation analysis of single-molecule trajectories of the fluorescence signal detected in the donor and acceptor detection channels and vice versa shows an anticorrelated exponential decay and growth, respectively. (2) The time difference, Tg - Tr, of the mean observation times of all photons detected for the donor and acceptor detection channels within a single-molecule fluorescence burst allows one to identify and exclude molecules with an event of acceptor photobleaching. The presented single-molecule analysis methods can be constrained to, for example, FRET-active subpopulations, reducing bias from FRET-inactive molecules. The observations made are of strong relevance for and demand a careful choice of laser action in multicolor and FRET experiments, in particular when performed at or close to saturation. Analysis of Photobleaching in Single-Molecule Multicolor Excitation and Förster Resonance Energy Transfer Measurements C Eggeling J Widengren L Brand J Schaffer S Felekyan CAM Seidel doi:10.1021/jp054581w J. Phys. Chem. A, Vol. 110, No. 9. (9 March 2006), pp. 2979-2995. 2008-06-16T18:12:34-00:00 2006 J. Phys. Chem. A 110 9 2979 2995 fret photobleaching photochemistry photophysics http://www.citeulike.org/user/samjlord/article/2899201 <i>Appl. Opt., Vol. 44, No. 27. (2005), pp. 5675-5683.</i><br /><br />Mie theory can be used to generate full-color simulations of atmospheric glories, but it offers no explanation for the formation of glories. Simulations using the Debye series indicate that glories are caused by rays that have suffered one internal reflection within spherical droplets of water. In 1947, van de Hulst suggested that backscattering (i.e., scattering angle theta=180°) could be caused by surface waves, which would generate a toroidal wavefront due to spherical symmetry. Furthermore, he postulated that the glory is the interference pattern corresponding to this toroidal wavefront. Although van de Hulst's explanation for the glory has been widely accepted, the author offers a slightly different explanation. Noting that surface waves shed radiation continuously around the droplet (not just at theta=180°), scattering in a specific direction theta=180° - delta can be considered as the vector sum of two surface waves: one deflecting the incident light by 180° - delta and the other by 180° + delta. The author suggests that the glory is the result of two-ray interference between these two surface waves. Simple calculations indicate that this model produces more accurate results than van de Hulst's model. How are glories formed? Philip Laven Appl. Opt., Vol. 44, No. 27. (2005), pp. 5675-5683. 2008-06-16T17:42:03-00:00 2005 Appl. Opt. 44 27 5675 5683 OSA cpjc fun http://www.citeulike.org/user/samjlord/article/2883270 <i>Biophys. J. (6 June 2008), biophysj.108.131276.</i><br /><br />Quantitative analysis in Forster Resonance Energy Transfer (FRET) experiments in live cells for protein interaction studies is still a challenging issue. In a two component system (FRET and no FRET donor species), fitting of Fluorescence Lifetime Imaging Microscopy (FLIM) data gives the fraction of donor molecules involved in FRET (fD) and the intrinsic transfer efficiency. But when fast FLIM acquisitions are used to monitor dynamic changes in protein-protein interactions at high spatial and temporal resolution in living cells, photon statistic and time resolution is limited. In this case, fitting procedures are not reliable, even for single lifetime donors. We introduce the new concept of a minimal fraction of donor molecules involved in FRET (mfD), coming from the mathematical minimization of fD. We find particular advantage in the use of mfD because it can be obtained without fitting procedures and is derived directly from FLIM data. mfD constitutes an interesting quantitative parameter for live cell studies because it is related to the minimal relative concentration of interacting proteins. For multi lifetime donors, the process of fitting complex fluorescence decays in order to find at least four reliable lifetimes is a near impossible task. Here, mfD extension for multi lifetime donors is the only quantitative determinant. We applied this methodology for imaging the interaction between the bromodomains of TAFII250 and acetylated histones H4 in living cells at high resolution. We show the existence of discrete acetylated chromatin domains where the minimal fraction of bromodomain interacting with acetylated H4 oscillates from 0.26 to 0.36 and whose size is smaller than half of one micron cube. We demonstrate that mfD by itself is a useful tool to investigate quantitatively protein interactions in live cells, especially when using fast FRET-FLIM acquisition. 10.1529/biophysj.108.131276 Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells Sergi Padilla-Parra Nicolas Auduge Maite Coppey-Moisan Marc Tramier doi:10.1529/biophysj.108.131276 Biophys. J. (6 June 2008), biophysj.108.131276. 2008-06-11T15:29:31-00:00 2008 Biophys. J. biophysj.108.131276 flim fret http://www.citeulike.org/user/samjlord/article/2868203 <i>Nature, Vol. 453, No. 7196., pp. 757-760.</i> High-harmonic generation by resonant plasmon field enhancement Seungchul Kim Jonghan Jin Young-Jin Kim In-Yong Park Yunseok Kim Seung-Woo Kim doi:10.1038/nature07012 Nature, Vol. 453, No. 7196., pp. 757-760. 2008-06-06T03:01:26-00:00 Nature 0028-0836 453 7196 757 760 Nature Publishing Group laser sers http://www.citeulike.org/user/samjlord/article/2870105 <i>ACS Chem. Biol. (6 June 2008)</i><br /><br />We have designed a modular protein tagging system that allows different functionalities to be linked onto a single genetic fusion, either in solution, in living cells, or in chemically fixed cells. The protein tag (HaloTag) is a modified haloalkane dehalogenase designed to covalently bind to synthetic ligands (HaloTag ligands). The synthetic ligands comprise a chloroalkane linker attached to a variety of useful molecules, such as fluorescent dyes, affinity handles, or solid surfaces. Covalent bond formation between the protein tag and the chloroalkane linker is highly specific, occurs rapidly under physiological conditions, and is essentially irreversible. We demonstrate the utility of this system for cellular imaging and protein immobilization by analyzing multiple molecular processes associated with NF-ºB-mediated cellular physiology, including imaging of subcellular protein translocation and capture of proteinprotein and proteinDNA complexes. HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis Georgyi Los Lance Encell Mark Mcdougall Danette Hartzell Natasha Karassina Chad Zimprich Monika Wood Randy Learish Rachel Ohana Marjeta Urh Dan Simpson Jacqui Mendez Kris Zimmerman Paul Otto Gediminas Vidugiris Ji Zhu Aldis Darzins Dieter Klaubert Robert Bulleit Keith Wood doi:10.1021/cb800025k ACS Chem. Biol. (6 June 2008) 2008-06-06T17:18:18-00:00 2008 ACS Chem. Biol. bioconjugation http://www.citeulike.org/user/samjlord/article/2870072 <i>Science, Vol. 320, No. 5881. (6 June 2008), pp. 1332-1336.</i><br /><br />Fluorescence light microscopy allows multicolor visualization of cellular components with high specificity, but its utility has until recently been constrained by the intrinsic limit of spatial resolution. We applied three-dimensional structured illumination microscopy (3D-SIM) to circumvent this limit and to study the mammalian nucleus. By simultaneously imaging chromatin, nuclear lamina, and the nuclear pore complex (NPC), we observed several features that escape detection by conventional microscopy. We could resolve single NPCs that colocalized with channels in the lamin network and peripheral heterochromatin. We could differentially localize distinct NPC components and detect double-layered invaginations of the nuclear envelope in prophase as previously seen only by electron microscopy. Multicolor 3D-SIM opens new and facile possibilities to analyze subcellular structures beyond the diffraction limit of the emitted light. 10.1126/science.1156947 Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy Lothar Schermelleh Peter Carlton Sebastian Haase Lin Shao Lukman Winoto Peter Kner Brian Burke Cristina Cardoso David Agard Mats Gustafsson Heinrich Leonhardt John Sedat doi:10.1126/science.1156947 Science, Vol. 320, No. 5881. (6 June 2008), pp. 1332-1336. 2008-06-06T16:49:53-00:00 2008 Science 320 5881 1332 1336 super-resolution http://www.citeulike.org/user/samjlord/article/2851647 <i>J. Am. Chem. Soc., Vol. 126, No. 6. (18 February 2004), pp. 1741-1747.</i><br /><br />Abstract: Three new azo-benzene-based push-pull chromophores with dendritic architecture were synthesized as active materials for electro-optic applications. These chromophores were synthesized in six or seven synthetic steps with an overall yield of around 80% per step and high purity. UV-vis spectroscopy showed significant influence of the transient dipole moment on the observed r33 values. The chromophores were stable to photochemical oxidation in ambient light and air. The electrical poling conditions were optimized for each chromophore as the Tg of the composite material varied significantly. The highest EO coefficient achieved was 22-25 pm/V at 1550 nm wavelength. STEM analysis of the blends enabled the correlation of the activity of these large chromophores with the blend morphology. An amorphous polycarbonate host effectively disperses the chromophores in 2-20 nm aggregates in the active materials. However, macrophase separation into 200-500 nm aggregates was observed in a methacrylate host matrix. Star-Shaped Azo-Based Dipolar Chromophores: Design, Synthesis, Matrix Compatibility, and Electro-optic Activity P Gopalan HE Katz DJ Mcgee C Erben T Zielinski D Bousquet D Muller J Grazul Y Olsson doi:10.1021/ja039768k J. Am. Chem. Soc., Vol. 126, No. 6. (18 February 2004), pp. 1741-1747. 2008-05-31T02:28:38-00:00 2004 J. Am. Chem. Soc. 126 6 1741 1747 dcdhf nlo http://www.citeulike.org/user/samjlord/article/2845997 <i>J. Am. Chem. Soc. (29 May 2008)</i><br /><br />Abstract: Determining how proteins fold into their native structures is a subject of great importance, since ultimately it will allow protein structure and function to be predicted from primary sequence data. In addition, there is now a clear link between protein unfolding and misfolding events and many disease states. However, since proteins fold over rugged, multidimensional energy landscapes, this is a challenging experimental and theoretical problem. Single-molecule fluorescence methods developed over the past decade have the potential to follow the unfolding/folding of individual molecules. Mapping out the landscape without ensemble averaging will enable the identification of intermediate states which may not be significantly populated, in addition to the presence of multiple pathways. To date, there have been only a limited number of single-molecule folding/unfolding studies under nonequilibrium conditions and no intermediates have been observed. Here, for the first time, we present a single-molecule study of the unfolding of a large autofluorescent protein, Citrine, a variant of green fluorescent protein. Single-molecule fluorescence techniques are used to directly detect an intermediate on the unfolding/folding pathway and the existence of parallel unfolding pathways. This work, and the novel methods used, shows that single-molecule fluorescence can now provide new, hitherto experimentally inaccessible, insights into the folding/unfolding of proteins. Evidence of an Intermediate and Parallel Pathways in Protein Unfolding from Single-Molecule Fluorescence Angel Orte Timothy Craggs Samuel White Sophie Jackson David Klenerman doi:10.1021/ja709973m J. Am. Chem. Soc. (29 May 2008) 2008-05-29T22:56:09-00:00 2008 J. Am. Chem. Soc. fret proteins sms http://www.citeulike.org/user/samjlord/article/2837703 <i>Nature methods (18 May 2008)</i><br /><br />The resolution of any linear imaging system is given by its point spread function (PSF) that quantifies the blur of an object point in the image. The sharper the PSF, the better the resolution is. In standard fluorescence microscopy, however, diffraction dictates a PSF with a cigar-shaped main maximum, called the focal spot, which extends over at least half the wavelength of light (lambda = 400-700 nm) in the focal plane and >lambda along the optical axis (z). Although concepts have been developed to sharpen the focal spot both laterally and axially, none of them has reached their ultimate goal: a spherical spot that can be arbitrarily downscaled in size. Here we introduce a fluorescence microscope that creates nearly spherical focal spots of 40-45 nm (lambda/16) in diameter. Fully relying on focused light, this lens-based fluorescence nanoscope unravels the interior of cells noninvasively, uniquely dissecting their sub-lambda-sized organelles. Spherical nanosized focal spot unravels the interior of cells. Roman Schmidt Christian A Wurm Stefan Jakobs Johann Engelhardt Alexander Egner Stefan W Hell doi:10.1038/nmeth.1214 Nature methods (18 May 2008) 2008-05-27T14:47:59-00:00 2008 Nature methods 1548-7105 super-resolution