Binding Stoichiometry and Affinity of Fluorescent Dyes to Proteins in Different Structural States

2012 ◽  
pp. 441-460 ◽  
Author(s):  
Anna I. Sulatskaya ◽  
Olga I. Povarova ◽  
Irina M. Kuznetsova ◽  
Vladimir N. Uversky ◽  
Konstantin K. Turoverov
Keyword(s):  
Fluorescent Dyes ◽  
Binding Stoichiometry

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Analysis of 3-d molecular distribution with the digital imaging microscope

1988 ◽  
Vol 46 ◽  
pp. 40-41
Author(s):  
W.A. Carrington ◽  
F.S. Fay ◽  
K.E. Fogarty ◽  
L. Lifshitz
Keyword(s):  
Image Restoration ◽  
Digital Imaging ◽  
Fluorescent Dyes ◽  
Optical Axis ◽  
Computer Hardware ◽  
Computer Algorithms ◽  
Low Contrast ◽  
Specific Proteins ◽  
Effective Use ◽  
Single Living Cells

Advances in digital imaging microscopy and in the synthesis of fluorescent dyes allow the determination of 3D distribution of specific proteins, ions, GNA or DNA in single living cells. Effective use of this technology requires a combination of optical and computer hardware and software for image restoration, feature extraction and computer graphics.The digital imaging microscope consists of a conventional epifluorescence microscope with computer controlled focus, excitation and emission wavelength and duration of excitation. Images are recorded with a cooled (-80°C) CCD. 3D images are obtained as a series of optical sections at .25 - .5 μm intervals.A conventional microscope has substantial blurring along its optical axis. Out of focus contributions to a single optical section cause low contrast and flare; details are poorly resolved along the optical axis. We have developed new computer algorithms for reversing these distortions. These image restoration techniques and scanning confocal microscopes yield significantly better images; the results from the two are comparable.

High-resolution measurement of birefringent fine structure in living cells using a new polarized light microscope

1995 ◽  
Vol 53 ◽  
pp. 54-55
Author(s):  
Rudolf Oldenbourg
Keyword(s):  
Light Microscope ◽  
Fluorescent Dyes ◽  
Polarized Light ◽  
Processing System ◽  
Video Camera ◽  
Molecular Organization ◽  
Computer Assisted ◽  
Image Recording ◽  
Birefringent Crystal ◽  
Technological Advances

The recent renaissance of the light microsope is fueled in part by technological advances in components on the periphery of the microscope, such as the laser as illumination source, electronic image recording (video), computer assisted image analysis and the biochemistry of fluorescent dyes for labeling specimens. After great progress in these peripheral parts, it seems timely to examine the optics itself and ask how progress in the periphery facilitates the use of new optical components and of new optical designs inside the microscope. Some results of this fruitful reflection are presented in this symposium.We have considered the polarized light microscope, and developed a design that replaces the traditional compensator, typically a birefringent crystal plate, with a precision universal compensator made of two liquid crystal variable retarders. A video camera and digital image processing system provide fast measurements of specimen anisotropy (retardance magnitude and azimuth) at ALL POINTS of the image forming the field of view. The images document fine structural and molecular organization within a thin optical section of the specimen.

En face dual fluorescence staining of fatty streaks allows observation of initiation and progression of atherosclerotic lesions

1995 ◽  
Vol 53 ◽  
pp. 864-865
Author(s):  
Anne M. Klinkner ◽  
Crystal R. Waites ◽  
Peter J. Bugelski ◽  
William D. Kerns
Keyword(s):  
Fluorescent Dyes ◽  
Nile Red ◽  
Dimethyl Formamide ◽  
High Cholesterol Diet ◽  
Methods Development ◽  
Atherosclerotic Lesions ◽  
En Face ◽  
Biochemical Evaluation ◽  
Stock Solutions ◽  
Dual Staining

A primary effort in the understanding of the progression of atherosclerotic disease has been methods development for visualization of the atherosclerotic plaque. We introduce a new method for the qualitative analysis of lipids in atherosclerotic fatty streaks which also retains those lipids for biochemical evaluation. An original aspect of the process is the ability to view an entire fatty streak en face, selectively stained for specific lipid classes within the lesion.New Zealand white rabbits were fed a high cholesterol diet(0.15%-0.3% for 14 wks). The aorta was removed and fixed in Carson's phosphate buffered formaldehyde followed by dual staining in the fluorescent dyes Nile red and filipin. Stock solutions of nile red(0.5mg/ml acetone) and filipin(2.5mg/ml dimethyl formamide) were prepared and kept at -20°C; all subsequent steps were at RT. 0.5cm × 1.0cm pieces of aorta were trimmed and adventitia removed. The pieces were then washed 3×15 min in PBS w/o CaMg, soaked in Nile red(NR)/filipin(Fl) stain(100(il NR stock + 200μl Fl stock in 10 ml PBS for 30 min, washed in PBS 3×30 min, rinsed with distilled water, mounted(Crystal Mount, Biomedia) and coverslipped and viewed by fluorescence microscopy.

Calcium ion imaging in plant cells

1993 ◽  
Vol 51 ◽  
pp. 132-133
Author(s):  
Peter K. Hepler ◽  
Dale A. Callaham
Keyword(s):  
Plant Cell Wall ◽  
Cytoplasmic Membrane ◽  
Fluorescent Dyes ◽  
Free Acid ◽  
Methyl Esters ◽  
Free Calcium ◽  
Local Concentration ◽  
Ion Imaging ◽  
Membrane Compartments ◽  
Free Acid Form

Calcium ions (Ca) participate in many signal transduction processes, and for that reason it is important to determine where these ions are located within the living cell, and when and to what extent they change their local concentration. Of the different Ca-specific indicators, the fluorescent dyes, developed by Grynkiewicz et al. (1), have proved most efficacious, however, their use on plants has met with several problems (2). First, the dyes as acetoxy-methyl esters are often cleaved by extracellular esterases in the plant cell wall, and thus they do not enter the cell. Second, if the dye crosses the plasma membrane it may continue into non-cytoplasmic membrane compartments. Third, even if cleaved by esterases in the cytoplasm, or introduced as the free acid into the cytoplasmic compartment, the dyes often become quickly sequestered into vacuoles and organelles, or extruded from the cell. Finally, the free acid form of the dye readily complexes with proteins reducing its ability to detect free calcium. All these problems lead to an erroneous measurement of calcium (2).

Morphogenetic machines revealed: Microscopy of living cells in the embryo of the frog, Xenopus laevis

1993 ◽  
Vol 51 ◽  
pp. 172-173
Author(s):  
Ray Keller
Keyword(s):  
Image Processing ◽  
Fluorescent Dyes ◽  
Cell Movement ◽  
Living Cells ◽  
Ease Of Use ◽  
Low Light ◽  
Amphibian Embryo ◽  
Large Populations ◽  
Light Fluorescence ◽  
Video Image Processing

The amphibian embryo offers advantages of size, availability, and ease of use with both microsurgical and molecular methods in the analysis of fundamental developmental and cell biological problems. However, conventional wisdom holds that the opacity of this embryo limits the use of methods in optical microscopy to resolve the cell motility underlying the major shape-generating processes in early development.These difficulties have been circumvented by refining and adapting several methods. First, methods of explanting and culturing tissues were developed that expose the deep, nonepithelial cells, as well as the superficial epithelial cells, to the view of the microscope. Second, low angle epi-illumination with video image processing and recording was used to follow patterns of cell movement in large populations of cells. Lastly, cells were labeled with vital, fluorescent dyes, and their behavior recorded, using low-light, fluorescence microscopy and image processing. Using these methods, the details of the cellular protrusive activity that drives the powerful convergence (narrowing)

Optical imaging probes and their potential contribution to radiotracer development

2016 ◽  
Vol 55 (02) ◽  
pp. 51-62 ◽  
Author(s):  
S. Hermann ◽  
M. Schäfers ◽  
C. Höltke ◽  
A. Faust
Keyword(s):  
Optical Imaging ◽  
Fluorescent Dyes ◽  
Great Influence ◽  
Potential Contribution ◽  
Preclinical Evaluation ◽  
Guided Surgery ◽  
Fluorescence Guided Surgery ◽  
Imaging Probes ◽  
Unspecific Binding

SummaryOptical imaging has long been considered a method for histological or microscopic investigations. Over the last 15 years, however, this method was applied for preclinical molecular imaging and, just recently, was also able to show its principal potential for clinical applications (e.g. fluorescence-guided surgery). Reviewing the development and preclinical evaluation of new fluorescent dyes and target-specific dye conjugates, these often show characteristic patterns of their routes of excretion and biodistribution, which could also be interesting for the development and optimization of radiopharmaceuticals. Especially ionic charges show a great influence on biodistribution and netcharge and charge-distribution on a conjugate often determines unspecific binding or background signals in liver, kidney or intestine, and other organs.Learning from fluorescent probe behaviour in vivo and translating this knowledge to radio-pharmaceuticals might be useful to further optimize emerging and existing radiopharmaceuticals with respect to their biodistribution and thereby availability for binding to their targets.

Enhanced Electroluminescence of Urethane Containing Processable Polythiophene Derivative by Addition of Dye Molecules

2000 ◽  
Vol 660 ◽  
Author(s):  
Amarjeet Kaur ◽  
Mario J. Cazeca ◽  
Kethinni G. Chittibabu ◽  
Jayant Kumar ◽  
Sukant K. Tripathy
Keyword(s):  
Fluorescent Dyes ◽  
Visible Region ◽  
Dye Molecules ◽  
Flat Panel Display ◽  
Large Area ◽  
Good Efficiency ◽  
Display Devices ◽  
Yellow Color ◽  
Organic Electroluminescent ◽  
Important Approach

ABSTRACTOrganic electroluminescent (EL) diodes based on fluorescent dyes and conducting polymers have attracted the interest of researchers, mainly because of their emission in the visible region and for application to large area portable flat panel display devices, driven at low voltages. Therefore, for the development of higher efficiency polymer EL diodes, the optimal combination of the merits of organic fluorescent dye molecules with that of conjugated polymer is an important approach. We report electroluminescence studies of polymer light emitting diodes (p-LEDs) fabricated with poly[2-(3-thienyl)ethanol n-butoxy carbonylmethyl urethane] (PURET) and its composite with 4-dicyanomethylene-2-methyl-6-(p-dimethylaminostyryl)-4H pyran (DCM) dye. These materials have been chosen in view of the fact that PURET exhibits a small overlap between emission and absorption spectra whereas DCM has a good efficiency of trapping both electrons as well as holes. Polyaniline has been utilized as hole injecting layer whereas tris-8-hydroxyquinoline-aluminum as electron injecting layer. Enhanced electroluminescence with bright yellow color has been observed in p-LEDs by the addition of dye.

Synthesis of Smart Mesoporous Materials

2003 ◽  
Vol 775 ◽  
Author(s):  
G.V.Rama Rao ◽  
Qiang Fu ◽  
Linnea K. Ista ◽  
Huifang Xu ◽  
S. Balamurugan ◽  
...  
Keyword(s):  
Mesoporous Silica ◽  
Mesoporous Materials ◽  
Fluorescent Dyes ◽  
Thermo Gravimetric Analysis ◽  
Molecular Transport ◽  
Solute Diffusion ◽  
Gravimetric Analysis ◽  
Stimuli Responsive ◽  
Porous Network ◽  
Hybrid Mesoporous Materials

AbstractThis study details development of hybrid mesoporous materials in which molecular transport through mesopores can be precisely controlled and reversibly modulated. Mesoporous silica materials formed by surfactant templating were modified by surface initiated atom transfer radical polymerization of poly(N-isopropyl acrylamide) (PNIPAAm) a stimuli responsive polymer (SRP) within the porous network. Thermo gravimetric analysis and FTIR spectroscopy were used to confirm the presence of PNIPAAm on the silica surface. Nitrogen porosimetry, transmission electron microscopy and X-ray diffraction analyses confirmed that polymerization occurred uniformly within the porous network. Uptake and release of fluorescent dyes from the particles was monitored by spectrofluorimetry and scanning laser confocal microscopy. Results suggest that the presence of PNIPAAm, a SRP, in the porous network can be used to modulate the transport of aqueous solutes. At low temperature, (e.g., room temperature) the PNIPAAm is hydrated and extended and inhibits transport of analytes; at higher temperatures (e.g., 50°C) it is hydrophobic and is collapsed within the pore network, thus allowing solute diffusion into or out of the mesoporous silica. The transition form hydrophilic to hydrophobic state on polymer grafted mesoporous membranes was determined by contact angle measurements. This work has implications for the development of materials for the selective control of transport of molecular solutes in a variety of applications.

Sulfonamides Are an Overlooked Class of Electron Donors in Luminogenic Luciferins and Fluorescent Dyes

2018 ◽  
Author(s):  
Deepak K. Sharma ◽  
Spencer T. Adams ◽  
Kate L. Liebmann ◽  
Adam Choi ◽  
Stephen Miller
Keyword(s):  
Fluorescent Dyes ◽  
Bright Light ◽  
Firefly Luciferase ◽  
Electron Donors ◽  
Light Emitting

Many fluorophores, and all bright light-emitting substrates for firefly luciferase, contain hydroxyl or amine electron donors. Here we show that sulfonamides can serve as replacements for these canonical groups. Unlike “caged” carboxamides, sulfonamide analogues enable bioluminescence, and sulfonamidyl luciferins, coumarins, rhodols, and rhodamines are fluorescent in water. Sulfonamide donors thus have previously unappreciated potential to expand the functional repertoire of luminescent molecules.

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