- Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein
Nathan C Shaner
Nat Biotechnol 22:1567-72. 2004
..Three monomers with distinguishable hues from yellow-orange to red-orange have higher quantum efficiencies...
- Fluorescence cross-correlation spectroscopy in living cells
Institute of Biophysics, Dresden University of Technology, Tatzberg 47 51, D 01307 Dresden, Germany
Nat Methods 3:83-9. 2006
..We consider FCCS in the context of fluorescence resonance energy transfer and multicolor imaging techniques and discuss application strategies and recent technical advances...
- Ultra-high resolution imaging by fluorescence photoactivation localization microscopy
Samuel T Hess
Department of Physics and Astronomy, University of Maine, Orono, ME 04469, USA
Biophys J 91:4258-72. 2006
..This new method suggests a means to address a significant number of biological questions that had previously been limited by microscope resolution...
- A photoactivatable GFP for selective photolabeling of proteins and cells
George H Patterson
Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
Science 297:1873-7. 2002
..Here, we use the photoactivatable GFP both as a free protein to measure protein diffusion across the nuclear envelope and as a chimera with a lysosomal membrane protein to demonstrate rapid interlysosomal membrane exchange...
- Mechanisms of tryptophan fluorescence shifts in proteins
J T Vivian
Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
Biophys J 80:2093-109. 2001
..The modeling of electrostatic interactions, including hydration, in proteins is vital to understanding function and structure, and this study helps to assess the effectiveness of current electrostatic models...
- Fluorescence correlation spectroscopy in living cells
Sally A Kim
Institute of Biophysics, Dresden University of Technology, Tatzberg 47 51, D 01307 Dresden, Germany
Nat Methods 4:963-73. 2007
..A discussion of advantages and disadvantages of one-photon versus two-photon excitation for FCS is available in Supplementary Methods online...
- Anomalous diffusion of proteins due to molecular crowding
Daniel S Banks
Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
Biophys J 89:2960-71. 2005
- Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one- and two-photon excitation
School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 USA
Biophys J 77:2251-65. 1999
..At comparable signal levels, 2PE minimizes photobleaching in spatially restrictive cellular compartments, thereby preserving long-term signal acquisition...
- Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots
Quantum Dot Corporation, 26118 Research Rd, Hayward, CA 94545, USA
Nat Biotechnol 21:41-6. 2003
..The results indicate that QD-based probes can be very effective in cellular imaging and offer substantial advantages over organic dyes in multiplex target detection...
- Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes
Robert K Neely
School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
Nucleic Acids Res 33:6953-60. 2005
..Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes that cannot be discerned from the present X-ray structures...
- Practical guidelines for dual-color fluorescence cross-correlation spectroscopy
BIOTEC, Department of Biophysics, Dresden University of Technology, Tatzberg 47 51, D 01307 Dresden, Germany
Nat Protoc 2:2842-56. 2007
..It is a technique that is expected to see new applications in various fields of biochemical and cell biological research...
- Detection of quadruplex DNA structures in human telomeres by a fluorescent carbazole derivative
Cheng Chung Chang
Institute of Atomic and Molecular Sciences, Academia Sinica, P O Box 23 166, Taipei, 106, Taiwan, Republic of China
Anal Chem 76:4490-4. 2004
..Together these results provide the first evidence for the presence of quadruplex structures in human telomeres...
- Photodynamics of red fluorescent proteins studied by fluorescence correlation spectroscopy
Department of Biophysics, University of Ulm, Ulm, Germany
Biophys J 86:384-94. 2004
..These observations underscore the intimate connection between protein motions and photophysical processes in fluorescent proteins...
- Networks of gold nanoparticles and bacteriophage as biological sensors and cell-targeting agents
Glauco R Souza
University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 103:1215-20. 2006
..Together, the physical and biological features within these targeted networks offer convenient multifunctional integration within a single entity with potential for nanotechnology-based biomedical applications...
- Structural analysis of human serum albumin complexes with cationic lipids
Departement de Chimie Biologie, Universite du Quebec a Trois Rivieres, C P 500, Trois Rivieres, Quebec, G9A 5H7, Canada
J Phys Chem B 113:1777-84. 2009
..HSA conformation was stabilized by cholesterol and DOPE with a slight increase of protein alpha-helical structures, while DOTAP and DDAB induced an important (alpha-->beta) transition, suggesting a partial protein unfolding...
- Fluorescent pteridine nucleoside analogs: a window on DNA interactions
M E Hawkins
Pediatric Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
Cell Biochem Biophys 34:257-81. 2001
..The two guanosine analogs, 3MI and 6MI, and two adenosine analogs, 6MAP and DMAP, are reviewed in detail along with applications utilizing them...
- Digital PCR
The Howard Hughes Medical Institute and The Johns Hopkins Oncology Center, Baltimore, MD 21231, USA
Proc Natl Acad Sci U S A 96:9236-41. 1999
..The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample...
- Intercalating nucleic acids containing insertions of 1-O-(1-pyrenylmethyl)glycerol: stabilisation of dsDNA and discrimination of DNA over RNA
Ulf B Christensen
Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK 5230 Odense M, Denmark
Nucleic Acids Res 30:4918-25. 2002
..Fluorescence measurements show a stronger interaction of the pyrene moiety with DNA than with RNA, indicating intercalation as the stabilising factor in DNA/INA duplexes...
- A rapid bioassay for single bacterial cell quantitation using bioconjugated nanoparticles
Center for Research at the Bio Nano Interface, Department of Chemistry, and The Shands Cancer Center, University of Florida, Gainesville, FL 32611, USA
Proc Natl Acad Sci U S A 101:15027-32. 2004
..The ultimate power of integrating bionanotechnology into complex biological systems will emerge as a revolutionary tool for ultrasensitive detection of disease markers and infectious agents...
- HIV-1 nucleocapsid protein as a nucleic acid chaperone: spectroscopic study of its helix-destabilizing properties, structural binding specificity, and annealing activity
Maria A Urbaneja
AIDS Vaccine Program, SAIC Frederick, Building 535 424, National Cancer Institute Frederick, Frederick, MD 21702 1201, USA
J Mol Biol 318:749-64. 2002
- Investigation of the dimerization of proteins from the epidermal growth factor receptor family by single wavelength fluorescence cross-correlation spectroscopy
Department of Chemistry, National University of Singapore, Singapore
Biophys J 93:684-98. 2007
..These receptors are major targets of anti-cancer drug development, and the receptors' homo- and heterodimeric structures are relevant for such developments...
- How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription
Unite de Pharmacologie Chimique et Genetique, CNRS, UMR 8151, INSERM, U 640, Paris, F 75270 cedex 06, France
J Mol Biol 383:1112-28. 2008
..Moreover, the weakening of the upper base pair of the stem likely promotes the melting of the stem that is required to convert the kissing complex into the final (+/-)PBS extended duplex...
- Real-time DNA sequencing from single polymerase molecules
Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA
Science 323:133-8. 2009
..Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates...
- Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET Förster radius
Gert Jan Kremers
Section Molecular Cytology and Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 316, 1098 SM, Amsterdam, The Netherlands
Biochemistry 45:6570-80. 2006
..Using the large lifetime difference between SCFP1 and SCFP3A enabled us to perform for the first time dual-lifetime imaging of spectrally identical fluorescent species in living cells...
- Quantum dot bioconjugates for imaging, labelling and sensing
Igor L Medintz
Center for Bio Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
Nat Mater 4:435-46. 2005
..The potential of QDs in biology has just begun to be realized and new avenues will arise as our ability to manipulate these materials improves...
- Mapping dynamic protein interactions in MAP kinase signaling using live-cell fluorescence fluctuation spectroscopy and imaging
Brian D Slaughter
Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
Proc Natl Acad Sci U S A 104:20320-5. 2007
..These results provide a quantitative spatial map of MAPK complexes in vivo and directly support the model that membrane association and regulation of the Ste5 scaffold are critical steps in MAPK activation...
- Biological and chemical applications of fluorescence correlation spectroscopy: a review
Samuel T Hess
Department of Physics and School of Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, New York 14853, USA
Biochemistry 41:697-705. 2002
- Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 104:12610-5. 2007
..The high level of selectivity of incoming dNTPs pertinent to this conformational change is a major contributor to replicative fidelity...
- Quantification of alpha-synuclein binding to lipid vesicles using fluorescence correlation spectroscopy
School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 2501, USA
Biophys J 90:4692-700. 2006
..Our results demonstrate that fluorescence correlation spectroscopy provides a powerful tool for the quantitative characterization of alphaS-lipid interactions...
- Selenium speciation by high-performance anion-exchange chromatography-post-column UV irradiation coupled with atomic fluorescence spectrometry
State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco Environmental Sciences, Chinese Academy of Sciences, P O Box 2871, Beijing 100085, China
J Chromatogr A 1118:139-43. 2006
..was established in this paper using high-performance anion-exchange chromatography coupled with atomic fluorescence spectrometry (HPAEC-AFS)...
- Structural characterization and immunogenicity in wild-type and immune tolerant mice of degraded recombinant human interferon alpha2b
Central Laboratory Animal Institute, Utrecht University, Utrecht, The Netherlands
Pharm Res 22:1997-2006. 2005
..This study was conducted to study the influence of protein structure on the immunogenicity in wild-type and immune tolerant mice of well-characterized degradation products of recombinant human interferon alpha2b (rhIFNalpha2b)...
- Probing protein oligomerization in living cells with fluorescence fluctuation spectroscopy
School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA
Proc Natl Acad Sci U S A 100:15492-7. 2003
..Resolving protein interactions in a cell is an important step in understanding cellular function on a molecular level. Brightness analysis promises to develop into an important tool for determining protein complex formation in cells...
- Online fluorescent dye detection method for the characterization of immunoglobulin G aggregation by size exclusion chromatography and asymmetrical flow field flow fractionation
Division of Drug Delivery Technology, Leiden Amsterdam Center for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
Anal Biochem 378:115-22. 2008
..The developed online fluorescent dye detection for HP-SEC or AF4 with Bis-ANS is a powerful method to detect both aggregation and structural changes of both monomeric and aggregated IgG in heat-stressed formulations...
- Attomolar sensitivity in bioassays based on surface plasmon fluorescence spectroscopy
Max Planck Institute for Polymer Research, Ackermannweg 10, D 55128 Mainz, Germany
J Am Chem Soc 126:8902-3. 2004
..Time-resolved ultratrace detection of fluorophore (Alexa-Fluor 647)-labeled rabbit anti-mouse antibody down to 500 aM (10-18 M) was accomplished, corresponding to a binding rate of approximately 10 molecules mm-2 min-1...
- Fluorescence resonance energy transfer as a probe for G-quartet formation by a telomeric repeat
J L Mergny
Laboratoire de Biophysique, Museum national d histoire naturelle, INSERM U 201, CNRS UMR 8646, 43 rue Cuvier, 75005 Paris, France
Chembiochem 2:124-32. 2001
..The folding of the G-quartet could be followed at concentrations as low as 100 pM. Fluorescence resonance energy transfer can thus be used to reveal the formation of multistranded DNA structures...
- Catalytic activation of human glucokinase by substrate binding: residue contacts involved in the binding of D-glucose to the super-open form and conformational transitions
Department of Clinical Medicine, University of Bergen, Norway
FEBS J 275:2467-81. 2008
- Spectroscopic and structural study of proton and halide ion cooperative binding to gfp
Scuola Normale Superiore, National Enterprise for nanoScience and nanoTechnology Consiglio Nazionale delle Ricerche Instituto Nazionale di Fisica della Materia, Pisa, Italy
Biophys J 93:232-44. 2007
..halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed...
- Sequence-specific binding of human immunodeficiency virus type 1 nucleocapsid protein to short oligonucleotides
R J Fisher
Protein Chemistry Laboratory, SAIC Frederick, NCI Frederick Cancer Research and Development Center, Maryland 21702, USA
J Virol 72:1902-9. 1998
- Examining the proteins of functional retinal lipofuscin using proteomic analysis as a guide for understanding its origin
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
Mol Vis 11:1122-34. 2005
..To elucidate the origins of biologically active retinal lipofuscin (RLF) by examining its protein composition...
- Ethidium derivatives bind to G-quartets, inhibit telomerase and act as fluorescent probes for quadruplexes
Laboratoire de Biophysique, , INSERM U201, CNRS UMR 8646, 43 rue Cuvier, 75005 Paris, France
Nucleic Acids Res 29:1087-96. 2001
..This recognition was associated with telomerase inhibition in vitro: these derivatives showed a potent anti-telomerase activity, with IC(50) values of 18-100 nM in a standard TRAP assay...
- Mechanism of interaction between human serum albumin and N-alkyl phenothiazines studied using spectroscopic methods
P B Kandagal
Department of Chemistry, Karnatak University, Dharwad, India
J Pharm Biomed Anal 47:260-7. 2008
..The decreased binding constants of HAS-LMM and HAS-PPC systems in presence of common ions indicated the availability of higher concentration of free drug in plasma...
- The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
Proc Natl Acad Sci U S A 102:2385-9. 2005
..These measurements, which should be widely applicable to other systems, can provide important information about the still incompletely understood conformational properties of unfolded proteins and the mechanism of protein folding...
- A dynamic view of cellular processes by in vivo fluorescence auto- and cross-correlation spectroscopy
Experimental Biophysics Group, Max Planck Institut fur biophysikalische Chemie, Am Fassberg 11, D 37077, Gottingen, Germany
Methods 29:74-85. 2003
..Practical implications of nonideal conditions including incomplete focus overlap and spectral cross-talk are considered. Recent examples of both auto- and cross-correlation applications demonstrate the potential of FCS for cell biology...
- Two-photon image correlation spectroscopy and image cross-correlation spectroscopy
P W Wiseman
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0339, USA
J Microsc 200:14-25. 2000
..We also demonstrate cellular application of two-photon ICS for measurements of slow diffusion of green fluorescent protein/adhesion receptor constructs within the basal membrane of live CHO fibroblast cells...
- Emerging imaging techniques
Elliot R McVeigh
Laboratory of Cardiac Energetics, NHLBI, National Institutes of Health, Bethesda, MD, USA
Circ Res 98:879-86. 2006
..The techniques covered are: ultrasound biomicroscopy (UBM), microSPECT, microPET, near infrared imaging, and quantum dots. For each technique, the basic physical principles are explained and recent example applications demonstrated...
- Molecular beacons with intrinsically fluorescent nucleotides
Angel A Marti
Department of Chemistry, Columbia University, New York, NY 10027, USA
Nucleic Acids Res 34:e50. 2006
..The thermal denaturation profile of MB-FB hybridized with its target shows a marked fluorescence reduction at 53 degrees C, consistent with a transition from double stranded helix to random coil DNA...
- Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution
Department of Biochemical Kinetics, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
Biophys J 72:1878-86. 1997
..The concentration of the reaction product can be directly determined from the cross-correlation amplitude...
- Antibody response to aggregated human interferon alpha2b in wild-type and transgenic immune tolerant mice depends on type and level of aggregation
Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences UIPS, Utrecht University, P O BOX 80082, 3508 TB Utrecht, The Netherlands
J Pharm Sci 95:1084-96. 2006
..In conclusion, the transgenic mouse model can be used to screen rhIFNalpha2b formulations for low levels of immunogenic aggregates obtained under accelerated storage conditions...
- Interaction of EGF receptor and grb2 in living cells visualized by fluorescence resonance energy transfer (FRET) microscopy
Department of Pharmacology, University of Colorado Health Sciences Center, Denver, Colorado 80111, USA
Curr Biol 10:1395-8. 2000
..The work also highlights the potential of FRET microscopy in the study of subcellular compartmentalization of protein-protein interactions in living cells...
- Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons
Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Toyama 930 0194, Japan
J Org Chem 69:3271-5. 2004
..Advantages of the excimer-monomer switching molecular beacons were discussed in comparison with conventional ones...
- RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloid coralyne
Md Maidul Islam
Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology Council of Scientific and Industrial Research, 4 Raja S C Mullick Road, Kolkata 700032, India
Mol Biosyst 5:244-54. 2009
..Docking studies provided further insights into the partially intercalated state of coralyne inside the t-RNA structure. This study presents a complete binding and thermodynamic profile of coralyne interaction to t-RNA...
- Promoter clearance by T7 RNA polymerase. Initial bubble collapse and transcript dissociation monitored by base analog fluorescence
Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
J Biol Chem 277:2725-31. 2002
..They further indicate that initial bubble collapse precedes dissociation of the 5' end of the RNA...
- Enzymatic signal amplification of molecular beacons for sensitive DNA detection
Jianwei Jeffery Li
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
Nucleic Acids Res 36:e36. 2008
..Moreover, the extended version provides one additional level of signal amplification, bringing the detection limit down to tens of femtomolar, nearly five orders of magnitude lower than that of conventional hybridization assay...
- Detection and imaging of zinc secretion from pancreatic beta-cells using a new fluorescent zinc indicator
Kyle R Gee
Molecular Probes, Inc, 4849 Pitchford Avenue, Eugene, Oregon 97402, USA
J Am Chem Soc 124:776-8. 2002
..Also, within secreting cells some regions of the cell membrane gave rise to secretion while others did not, suggesting active zones of secretion on the cell surface...
- Function and assembly of the bacteriophage T4 DNA replication complex: interactions of the T4 polymerase with various model DNA constructs
Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
J Biol Chem 278:25435-47. 2003
..We suggest that changes in the kinetics and thermodynamics of these steps by auxiliary replication proteins constitute a basic mechanism for protein coupling within the replication complex...
- Mechanism of nucleocapsid protein catalyzed structural isomerization of the dimerization initiation site of HIV-1
Manuela J Rist
Center for Advanced Research in Biotechnology of the University of Maryland, Rockville 20850, USA
Biochemistry 41:14762-70. 2002
- Probing dynamics of HIV-1 nucleocapsid protein/target hexanucleotide complexes by 2-aminopurine
S V Avilov
Institut Gilbert Laustriat, UMR 7175 CNRS Université Louis Pasteur Strasbourg I, Dépt Pharmacologie et Physicochimie, Faculte de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
Nucleic Acids Res 36:885-96. 2008
..Since this platform supports the NC chaperone properties, the restriction of the local mobility of the bases is likely a mechanistic component of these properties...
- Fluorescence resonance energy transfer microscopy: a mini review
University of Virginia, W M Keck Center for Cellular Imaging, Department of Biology, Gilmer Hall, Charlottesville, Virginia 22904, USA
J Biomed Opt 6:287-91. 2001
..This paper will provide a brief review of the above-mentioned FRET techniques...
- Molecular brightness characterization of EGFP in vivo by fluorescence fluctuation spectroscopy
Department of Physics, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
Biophys J 82:133-44. 2002
..We found the molecular brightness of EGFP to be a very robust parameter, and anticipate the use of PCH analysis for the study of oligomerization processes in vivo...
- Spatial-temporal studies of membrane dynamics: scanning fluorescence correlation spectroscopy (SFCS)
Department of Biophysics, University of Illinois in Urbana Champaign, Urbana, IL, USA
Biophys J 87:1260-7. 2004
..Scanning FCS provided a simple, quantitative, yet highly sensitive method to study protein-membrane interactions...
- An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells
Department of Physics, Princeton University, Princeton, NJ 08544, USA
Science 287:1652-5. 2000
..This experimental approach can be extended to quantitative in vivo studies of other biochemical networks...
- Using GFP in FRET-based applications
B A Pollok
Aurora Biosciences Corporation, San Diego, CA 92121, USA
Trends Cell Biol 9:57-60. 1999
..This review summarizes the use of GFP for FRET and illustrates the theme with specific examples on how GFP has been employed as an intracellular molecular sensor...
- Interaction of beta-lactoglobulin with resveratrol and its biological implications
Chaire de recherche du Canada sur les proteines, les bio systemes et les aliments fonctionnels, Institut de recherche sur les nutraceutiques et les aliments fonctionnels INAF STELA, Universite Laval, Sainte Foy, Canada
Biomacromolecules 9:50-6. 2008
..Complexing with beta-LG provides a slight increase in the photostability of resveratrol and a significant increase in its hydrosolubility...
- Green fluorescent protein variants as ratiometric dual emission pH sensors. 1. Structural characterization and preliminary application
George T Hanson
Department of Chemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 1229, USA
Biochemistry 41:15477-88. 2002
..Given their favorable optical characteristics, suitable pK(a)'s for the physiological pH range, and suitability for ratiometric measurements, dual emission GFPs should make excellent probes for studying pH in vivo...
- Direct measurement of Gag-Gag interaction during retrovirus assembly with FRET and fluorescence correlation spectroscopy
Daniel R Larson
School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
J Cell Biol 162:1233-44. 2003
..These methods also have general applicability to in vivo studies of protein-protein and -membrane interactions involved in the formation of complex macromolecular structures...
- Low-energy circular dichroism of 2-aminopurine dinucleotide as a probe of local conformation of DNA and RNA
Neil P Johnson
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 1229, USA
Proc Natl Acad Sci U S A 101:3426-31. 2004
..We have used this CD signal to provide information about the conformation of the AP dinucleotide at a defined position within single- and double-stranded nucleic acids...
- Conformational instability of the cholera toxin A1 polypeptide
Abhay H Pande
Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, FL 32826, USA
J Mol Biol 374:1114-28. 2007
..Thermal instability in the reduced CTA1 polypeptide has not been reported before, yet both the translocation and degradation of CTA1 may depend upon this physical property...
- Binding of ricin A-chain to negatively charged phospholipid vesicles leads to protein structural changes and destabilizes the lipid bilayer
Philip J Day
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, U K
Biochemistry 41:2836-43. 2002
..RTA also released trapped calcein from POPG vesicles, indicating that it destabilized the lipid bilayer. We speculate that membrane-induced partial unfolding of RTA during cell entry may facilitate its recognition as an ERAD substrate...
- Flavonoid-serum albumin complexation: determination of binding constants and binding sites by fluorescence spectroscopy
UMR A408 Institut National de la Recherche Agronomique, Universite d Avignon, Safety and Quality of Plant Products Agroparc, 84914 Avignon Cedex 9, France
Biochim Biophys Acta 1721:164-73. 2005
..Significant differences in affinity and binding location are observed for the highly homologous HSA and BSA...
- Inter- and intramolecular fluorescence quenching of organic dyes by tryptophan
Physikalisch Chemisches Institut, Universitat Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
Bioconjug Chem 14:1133-9. 2003
..Changes in the fluorescence quantum yield of dye-labeled peptides and proteins might be used advantageously for the quantification of proteases and specific binding partners...
- The effect of non-enzymatic glycation on the unfolding of human serum albumin
Deanna L Mendez
Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
Arch Biochem Biophys 444:92-9. 2005
..These results showed that glycation altered the local structure around Trp-214 while not significantly impacting the secondary structure, and this alteration translated into an overall change in the stability of gHSA compared to HSA...
- Fluorescence resonance energy transfer between quantum dot donors and dye-labeled protein acceptors
Aaron R Clapp
Optical Sciences Division, Code 5611, U S Naval Research Laboratory, Washington, D C 20375, USA
J Am Chem Soc 126:301-10. 2004
- Characterization of the mangiferin-human serum albumin complex by spectroscopic and molecular modeling approaches
Department of Chemistry, Lanzhou University, Lanzhou 730000, PR China
J Pharm Biomed Anal 49:753-9. 2009
..Computational mapping of the possible binding sites of mangiferin revealed the molecule to be bound in the large hydrophobic cavity of subdomain IIA...
- Assessment of bile fluorescence patterns in a tropical fish, Nile tilapia (Oreochromis niloticus) exposed to naphthalene, phenanthrene, pyrene and chrysene using fixed wavelength fluorescence and synchronous fluorescence spectrometry
Department of Zoology, Faculty of Science, University of Kelaniya, Kelaniya, Sri Lanka
Bull Environ Contam Toxicol 84:554-8. 2010
..This study supports the use of bile fluorescence in Nile tilapia by fixed wavelength fluorescence and synchronous fluorescence spectrometry with non-normalized data as a simple method for screening bioavailability of these PAHs.
- High sensitivity of Stark-shift voltage-sensing dyes by one- or two-photon excitation near the red spectral edge
Department for Biomedical Optics, Max Planck Institute for Medical Research, Heidelberg, Germany
Biophys J 87:631-9. 2004
..Such fractional sensitivities are approximately 5 times larger than what is commonly found with other voltage-sensing dyes and approach the theoretical limit given by the spectral Boltzmann tail...
- Structure of the DNA binding domain of E. coli SSB bound to ssDNA
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Campus Box 8231, 660 S Euclid Ave, Saint Louis, Missouri 63110, USA
Nat Struct Biol 7:648-52. 2000
..8 A. This structure describes the vast network of interactions that results in the extensive wrapping of single stranded DNA around the SSB tetramer and suggests a structural basis for its various binding modes...
- Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells
J C Politz
Worcester Foundation for Biomedical Research, University of Massachusetts Medical Center, Worcester Foundation Campus, Shrewsbury, MA 01545, USA
Proc Natl Acad Sci U S A 95:6043-8. 1998
..These results demonstrate that oligos can move about within the nucleus at rates comparable to those in aqueous solution and further suggest that this is true for large ribonucleoprotein complexes as well...
- Analyzing intracellular binding and diffusion with continuous fluorescence photobleaching
Division Biophysics of Macromolecules, German Cancer Research Center, D 69120 Heidelberg, Germany
Biophys J 84:3353-63. 2003
..The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of approximately 13 s...
- Novel, isotype-specific sensors for protein kinase A subunit interaction based on bioluminescence resonance energy transfer (BRET)
University of Kassel, Department of Biochemistry, Heinrich Plett Str 40, D 34132 Kassel, Germany
Cell Signal 18:1616-25. 2006
- DNA cytosine C5 methyltransferase Dnmt1: catalysis-dependent release of allosteric inhibition
Zeljko M Svedruzić
Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
Biochemistry 44:9472-85. 2005
..We describe limitations in the Michaelis-Menten kinetic analysis of Dnmt1 and suggest alternative approaches...
- Temperature-dependent simultaneous ligand binding in human serum albumin
Sudarson Sekhar Sinha
Unit for Nano Science and Technology, Department of Chemical, Biological and Macromolecular Sciences, SN Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
J Phys Chem B 112:4884-91. 2008
..From the FRET studies, an attempt has been made to characterize the simultaneous binding of the two ligands in various temperature-dependent folded states of HSA...
- The photon counting histogram in fluorescence fluctuation spectroscopy
Laboratory for Fluorescence Dynamics, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
Biophys J 77:553-67. 1999
- Simple fluorescent pyrimidine analogues detect the presence of DNA abasic sites
Nicholas J Greco
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
J Am Chem Soc 127:10784-5. 2005
..The most responsive of the family was incorporated in DNA. This isosteric fluorescent DNA analogue monitors denaturation of a DNA duplex via fluorescence and positively detects the presence of abasic sites in DNA duplexes...
- Cold vapour atomic fluorescence spectrometry and gas chromatography-pyrolysis-atomic fluorescence spectrometry for routine determination of total and organometallic mercury in food samples
Plymouth Environmental Research Centre, University of Plymouth, Drake Circus, Plymouth
Analyst 127:1108-14. 2002
..after nitric acid/peroxide digestion, evaporation of the solvent and detection by cold vapour-atomic fluorescence spectrometry. Full organomercury speciation requires a clean-up step before analysis of the final extract in ..
- A close look at fluorescence quenching of organic dyes by tryptophan
Applied Laser Physics and Laser Spectroscopy, University of Bielefeld, Universitatsstr 25, 33615 Bielefeld, Germany
Chemphyschem 6:2277-85. 2005
- Peculiar 2-aminopurine fluorescence monitors the dynamics of open complex formation by bacteriophage T7 RNA polymerase
R P Bandwar
Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
J Biol Chem 276:14075-82. 2001
..Thus, in the absence of the initiating nucleotide, GTP, the overall equilibrium constant for closed to open complex conversion is 0.5 and the net rate of open complex formation is nearly 150 s(-1)...
- Whole-body fluorescence lifetime imaging of a tumor-targeted near-infrared molecular probe in mice
Washington University School of Medicine, Department of Radiology, St Louis, Missouri 63110, USA
J Biomed Opt 10:054003. 2005
..This study clearly demonstrated the feasibility of whole-body NIR fluorescence lifetime imaging for tumor localization and its spatial functional status in living small animals...
- The LSM 510 META - ConfoCor 2 system: an integrated imaging and spectroscopic platform for single-molecule detection
Carl Zeiss Jena GmbH, Carl Zeiss Promenade 10, 07745 Jena, Germany
Curr Pharm Biotechnol 5:135-54. 2004
..In addition, we outline the calibration of the instrument and the work flow for data analysis with emphasis on in vivo pharmacological applications...
- Simultaneous speciation analysis of Sb(III), Sb(V) and (CH3)3SbCl2 by high performance liquid chromatography-hydride generation-atomic fluorescence spectrometry detection (HPLC-HG-AFS): application to antimony speciation in sea water
Ida De Gregori
Laboratorio de Química Analítica y Ambiental, Instituto de Quimica, Pontificia Universidad Catolica de Valparaiso, Avenida Brasil 2950, P O Box 4059, Valparaiso, Chile
J Chromatogr A 1091:94-101. 2005
..species by high performance liquid chromatography (HPLC) and its detection by hydride generation-atomic fluorescence spectrometry (HG-AFS)...
- Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission
Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University and SORST, Japan Science and Technology Corporation, Kyoto 615 8510, Japan
J Am Chem Soc 126:8364-5. 2004
..This method is useful for the determination of the presence/absence of insertion polymorphisms located at a specific site on the target DNA...
- Simultaneous determination of levodopa and carbidopa by synchronous fluorescence spectrometry using double scans
Wook Hyun Kim
Department of Chemistry, Kyungpook National University, Taegu 702 701, Republic of Korea
Anal Chim Acta 619:2-7. 2008
..006 microg mL(-1) for carbidopa and levodopa, respectively. The method was successfully applied to the determination of levodopa and carbidopa in pharmaceutical formulation and urine sample. The recovery results were satisfactory...
- Indirect determination of sulfide at ultratrace levels in natural waters by flow injection on-line sorption in a knotted reactor coupled with hydride generation atomic fluorescence spectrometry
School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry and Key Laboratory of MOE for Life Science, Nanjing University, Nanjing 210093, China
Anal Chem 79:7176-81. 2007
..reactor (KR) was developed for flow injection on-line sorption coupled with hydride generation atomic fluorescence spectrometry (HG-AFS). With the Hg2+ pH kept at 2...
- Kinetic stabilization of the alpha-synuclein protofibril by a dopamine-alpha-synuclein adduct
K A Conway
Center for Neurologic Diseases, Brigham and Women s Hospital, Department of Neurology, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
Science 294:1346-9. 2001
..Adduct formation provides an explanation for the dopaminergic selectivity of alpha-synuclein-associated neurotoxicity in PD and has implications for current and future PD therapeutic and diagnostic strategies...
- Fluorescence spectroscopy of single biomolecules
Materials Sciences and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Science 283:1676-83. 1999
..The progress in applying these tools to biological studies with the use of fluorophores that are site-specifically attached to macromolecules is reviewed...
- In vivo cancer targeting and imaging with semiconductor quantum dots
Department of Biomedical Engineering, and the Winship Cancer Institute, Emory University and Georgia Institute of Technology, 1639 Pierce Drive, Suite 2001, Atlanta, Georgia 30322, USA
Nat Biotechnol 22:969-76. 2004
..These results raise new possibilities for ultrasensitive and multiplexed imaging of molecular targets in vivo...
- EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion
Department of General Zoology and Endocrinology, University of Ulm, 89069 Ulm, Germany
Proc Natl Acad Sci U S A 101:15905-10. 2004
..The possibility to locally change the emission wavelength by focused UV light makes EosFP a superb marker for experiments aimed at tracking the movements of biomolecules within the living cell...
- Oligomeric assembly of native-like precursors precedes amyloid formation by beta-2 microglobulin
Catherine M Eakin
Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520 8114, USA
Biochemistry 43:7808-15. 2004
..The native-like structure and discrete oligomeric size of beta2m amyloid intermediates suggest that this protein forms fibrils by structural domain swapping...
- Speciation analysis of mercury in sediments, zoobenthos and river water samples by high-performance liquid chromatography hyphenated to atomic fluorescence spectrometry following preconcentration by solid phase extraction
Department of Chemistry and Biochemistry, Mendel University of Agriculture and Forestry, Zemedelska 1, Brno CZ 613 00, Czech Republic
Anal Chim Acta 615:115-23. 2008
..The limits of detection were 4.3microg L(-1) for methylmercury (MeHg(+)), 1.4microg L(-1) for ethylmercury (EtHg(+)), 0.8microg L(-1) for inorganic mercury (Hg(2+)), 0.8microg L(-1) for phenylmercury (PhHg(+))...
- Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix
Applied Laser Physics and Laser Spectroscopy, University of Bielefeld, Universitatsstrasse 25, 33615 Bielefeld, Germany
Proc Natl Acad Sci U S A 104:17400-5. 2007
- Direct determination of closely overlapping drug mixtures of diflunisal and salicylic acid in serum by means of derivative matrix isopotential synchronous fluorescence spectrometry
J A Murillo Pulgarin
Department of Analytical Chemistry and Foods Technology, University Castilla La Mancha, 13071 Ciudad Real, Spain
Anal Chim Acta 583:55-62. 2007
..The limit of detection calculated according to Clayton who uses error propagation throughout the calibration curve and a non-centralized security factor was 36.8 and 37.3 ng mL(-1) for diflunisal and salicylic acid, respectively...
- Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ indicator GCaMP2
Yvonne N Tallini
Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
Proc Natl Acad Sci U S A 103:4753-8. 2006
..d. 13.5, atrioventricular conduction through the canal was abolished at this stage. These studies demonstrate that GCaMP2 will have broad utility in the dissection of numerous complex cellular interactions in mammals, in vivo...