IgG Concentration Calculator. the extinction coefficient for the various transients we used the value of Cy5 at 645 nm ... Cy3B,13 Cy5B,1 Cy5, Cy5.5, Alexa 647,14 Cy7, and Alexa 750.14 R1 and R2 groups have been included due to structural differences observed from suppliers, however, other variations may be found. These values should be appreciated for what they are, and not accepted as constant under all conditions. Photochem. Cy3B as an internal Cy3B-dT; MW: 945 g/mol: Excitation maximum: 559 nm: Emission maximum: 570 nm: Extinction coefficient (260nm) 14.2 mM-1 cm-1 Like Cy3, Cy3B is most commonly paired with the dark quencher BHQ-2, as the two have excellent spectral overlap. Protein analysis is needed to determine if a sample solution contains the desired protein. Data from various sources including www.biosearchtech.com and www.glenresearch.com. Peptide tag N-terminal amine Biotinylation Quantum dot Large label so may interfere with activity. Learning Platform » Modifications » Fluorescent modifications » Cy3B. Hall, L.M., Gerowska, M., Brown, T. A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5, and Cy3B monomers. If no extinction coefficient information exists for a protein or protein mixture of interest, and a rough estimate of protein concentration is required for a solution that has no other interfering substances, assume εpercent = 10. Home » Invitrogen Cy3 dye is a bright, orange-fluorescent dye that can be excited using the 532 nm laser line and visualized with TRITC (tetramethylrhodamine) filter sets. Instrumentation Amersham Biosciences has devedetlhoep LEADseekerTM fluorescence … The on–off contrast is the brightness of the fluorophore in the ‘on’ state divided by that of the ‘off’ state. The molar extinction coefficient (ε) for Cy3B is 120,000 cm-1M-1 in PBS buffer. Cy3B dye can be incorporated at any position within an oligonucleotide post-synthetically. cm − 1, respectively ... Cy5 and Cy3B monomers. Cy3B fluorescent dye belongs to the Cyanine family of synthetic polymethine dyes. Cy3 dye. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Extinction Coeficient (ec) Technical Info (pdf) Absorbance MAX Emission MAX Absorbance EC. B.J. -20°C To -70°C Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Absorption and emission spectra of CF660R conjugated to goat antimouse IgG in PBS. Unless otherwise specified, molar extinction coefficient … 26-6907 ... Cy3B is reactive, water-soluble, has an absorbance maximum of 559 nm and an emission maximum of 570 nm. Therefore, a high extinction coefficient will lead to a greater amount of light being absorbed. As a result, Cy3B is both extremely bright and extremely stable. Bio-Synthesis offers Cy3B fluorescent dye oligonucleotide labeling. Our Scientific Applications Support team has assembled a list of frequently asked questions to help you find answers quickly. Sci., 8 (2009), pp. (2012), 40: e108. I'm really grateful to all of your answers. Contact us for CY3B fluorescent dye oligonucleotide labeling services. Bio-Synthesis Inc, 612 East Main Street Lewisville, TX 75057, Cy3b Fluorescent Dye Oligonucleotide Labeling. Each is defined as a photophysical parameter from a spectrophotometer or spectrofluorometer. CrossRef View Record in Scopus Google Scholar. Comparing eGFP with Cy3B, the relative brightness is 33,000 and 91,000, respectively, clearly showing that Cy3B is threefold brighter. Search molar extinction coefficient (ε) Select a compound from the list below to view molar extinction coefficient … Cooper, M., Ebner, A., Briggs, M., Burrows, M., Gardner, N., Richardson, R., West, R. Cy3B: improving the performance of cyanine dyes.J. J. Fluoresc. Reconstituted material may be stored for up to 2 weeks at -20° C in aliquots to avoid repeat freeze thaw cycles. This severely limits its use in the fields of genomics, biology and nanotechnology. E: extinction coefficient; Φ = quantum yield; τ = fluorescence lifetime. Metabion offers the Cy3B modification in its DNA portfolio. For example, measuring the absorbance of a protein sample at 280 nm with a spectrophotometer is a rapid and straightforward method. Nucleic Acid Extinction Coefficient of Nucleic Acid - ε base (M-1 cm-1) A 260 unit (µg/ml) dsDNA: 6,600: 50: ssDNA: 8,919: 33: DNA Oligo: 10,000: 33: RNA: 8,250: 40: ssRNA (21mer) 9,700: 33: Take me to Mirus Bio products. Dual HPLC purification is highly recommended. Cyanine dyes normally are capable of cis/trans isomerization around the polymethine, which can lead to loss of fluorescence after excitation, and weaker signal. As such, it does not incur into photo-isomerization events, and it is characterized by high stability and high degree of fluorescence emission. Filter using one or more categories to focus on specific topics, or use the search bar to perform a text search. Request PDF | Cy3B™: Improving the Performance of Cyanine Dyes | The spectral properties of a rigidified trimethine cyanine dye, Cy3B have been characterised. There are several different ε data sets which were frequently used in NIRS quantification. The results show excellent agreement with other recent observations to a long‐wavelength limit of about 1950 Å. where A 280 is the measured absorbance at 280 nm, A Cy3B,559 is the measured absorbance at the long-wavelength absorbance maximum of Cy3B (559 nm), A Alexa,652 is the measured absorbance at the long-wavelength absorbance maximum of Alexa647 (652 nm), ε P,280 is the molar extinction coefficient of RNAP σ 70 holoenzyme at 280 nm (240,000 M −1 cm −1), ε Cy3B,280 is the molar extinction coefficient of Cy3B … Application For the labelling of biological compounds with Cy3 ™ monofunctional dye. We have optimized the synthesis of Cy3B, and for the first time produced a diverse range of Cy3B monomers for use in solid-phase oligonucleotide synthesis. It has an absorbance maximum of 559 nm and an emission maximum of 570 nm. Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. Photobiol. However, Alexa Fluor 405 exhibits a relatively low brightness, which is typical for small organic UV and near-UV fluorophores The extinction coefficient is how well a dye absorbs at its absorption maximum. Cy3 can be detected by various fluorometers, imagers, and microscopes with standard filters for Tetramethylrhodamine (TRITC). Cy3B represents one isomer of the dye Cy3. The molar extinction coefficient (ε) for Cy3 (Cyanine-3) is 150,000 cm-1M-1 in PBS. Fluorescent protein GFP/RFP Single-molecule FRET Site-specific cysteine Cy3/Cy5 Single-molecule/particle tracking Single-molecule imaging Site-specific cysteine Cy3B Fluorophores can be spaced away from protein and targete dto inert areas. (2004), 14: 1145-150. Extinction coefficient (ε) is a critical parameter for quantification of oxy-, deoxy-, and total-hemoglobin concentrations (Δ[HbO2], Δ[Hb], Δ[tHb]) from optical measurements of Near-infrared spectroscopy (NIRS). Quantum yield is the ratio of photons emitted as fluorescence and the photons absorbed. The CO2 extinction coefficient in the 1700–3000 Å region has been measured using a 2‐m spectrometer in conjunction with a multiple‐path absorption cell. An oligonucleotide modified with a primary amine group is used to covalently attach dye with oligonucleotide via NHS ester chemistry; other cross-linking chemistries are also available depending on particular project specifications . Cy3B: improving the performance of cyanine dyes. • Each kind of fluorescent dye molecule absorbs maximally at a particular wavelength to an extent described by its extinction coefficient (ε´). Cyanine dyes normally are capable of cis/trans isomerization around the polymethine, which can lead to loss of fluorescence after excitation, and weaker signal. They are also environmentally insensitive. The CO 2 extinction coefficient in the 1700–3000 Å region has been measured using a 2‐m spectrometer in conjunction with a multiple‐path absorption cell. Cyanine-3b data from Cooper et al., Journal of Fluorescence 14 (2), 145-150, 2004. In addition to immunocytochemistry applications, Cy3 dye … Nucleic Acids Res., 40 (2012), p. e108. By contrast, Cy3B is conformationally locked, the dye is not subject to photo-isomerization and improved fluorescent properties1,2. J Chem Biol (2013) 6:85–95 DOI 10.1007/s12154-013-0094-5 REVIEW Fluorescent labeling and modification of proteins Christopher P. Toseland Received: 15 February 2013 / Accepted: 1 April 2013 / Published online: 13 April 2013 # Springer-Verlag Berlin Heidelberg 2013 The velocity of propagation of a electromagnetic wave through a solid is given by the frequency-dependent complex refractive index N = n - ik where the real part, n is related to the velocity, and k, the extinction coefficient is related to the decay, or damping of the oscillation amplitude of the incident electric field. (2004), 14: 1145-150, © metabion international AG / metabion GmbH 2018. Amersham Biosciences can synthesise combinations of fluorophores required for a FRET assay. The extinction coefficient is a measure of the ease in which a fluorophore absorbs light to enter the excited state. Unless otherwise specified, molar extinction coefficient (ε) values are typically measured in ddH2O or PBS. Cyanine dyes have large extinction coefficients, fluorescent lifetimes in the region of 1ns and are detected away from the natural autofluorescence of biomolecules. Harvey, C. Perez, M. LevitusDNA sequence-dependent enhancement of Cy3 fluorescence. Cy3B fluorescent dye belongs to the Cyanine family of synthetic polymethine dyes. Extinction coefficient: 72,000 cm-1M-1 Spectrally similar dyes: Fluorescein (FITC), Cy®2 Molecular weight: 720.66 Typical Conjugation Reaction The protein should be dissolved at a concentration of 50-100 µM in a suitable buffer (10-100 mM phosphate, Tris, or HEPES) at pH 7.0-7.5. 2b). The results show excellent agreement with other recent observations to a long‐wavelength limit of about 1950 Å. Extinction coefficient: 100,000 Molecular weight: ∼983 A 280/A max or CF (correction factor for estimating degree of protein labeling): 0.51 Flow cytometry laser line: 633, 635, or 640 nm Microscopy laser line: 633, 635, or 640 nm Direct replacement for: Alexa Fluor 660 Figure 1. Dye is fluorescein (FAM) or cyanine 3B (Cy3B) 15mer – 68 Å Dye-C 6-CGTGTGAATTCGTGC HS-C 6-GCACGAATTCACACG T m = 48.1 ºC, G 1 = -28.76kcal/mol, G 2 =-6.91kcal/mol 30mer – 117 Å Dye-C 6-CGCCTACTACCGAATTCGATAGTCATCAGC HS-C 6-GCTGATGACTATCGAATTCGGTAGTAGGCG T m = 61.3 ºC, G 1 = -56.65kcal/mol, G 2 =-5.19kcal/mol 45mer – 170 Å Dye-C 6 … Click here, M. Cooper, A. Ebner, M. Briggs, M. Burrows, N. Gardner, R. Richardson, and R. West. Extinction coefficients for proteins are determined at absorbance maxima near 280 nm. Newsletter. It is available as an NHS ester, and is used to fluorescently label oligonucleotides at either the 5- or 3-end, or internally. In fact, the expression extinction coefficient = extinction efficiency * A listed here is a mistake i have made. … Absorption and extinction coefficient theory. Most protein extinction coefficients (ε percent) range from 4.0 to 24.0. Moreover, Alexa Fluor 405 is directly available as NHS ester for the convenience of coupling to the amine-containing chelator heads. Go Back to Tips from the Bench. Cy3B can be used to substitute in any oligonucleotide-based application suitable for Cy3, such as TaqMan probes, Scorpion primers, Molecular Beacons, or Fluorescent In-Situ Hybridization. Fluoresc. more information about protein extinction coefficient (ε), including conversion between percent absorbances for a 1% solution and molar extinction coefficient, please see the related Tech Tip #6: Extinction coefficients. At 365 nm, this fluorophore retains ∼68% of its maximum molar extinction coefficient (Fig. Calibrated absorbance and fluorescence spectra and the Beer-Lambert law were used to determine the concentration of fluorophore and antibody for each conjugate [ 45 ]. - Cy3B. In this pH range, the protein thiol groups are sufficiently nucleophilic that they react almost exclusively with the reagent in … Cy3B absorbance was measured at 560 nm (Cy3B extinction coefficient = 130,000 M-1 cm-1), while AF647 absorbance was measured at 650 nm (AF647 extinction coefficient = 270,000 M-1 cm-1). Table 2: Extinction Coefficients and A 260 conversion units for nucleic acids. These parameters are in addition to general fluorophore properties to consider, including extinction coefficient, quantum yield, absorption and fluorescence wavelengths, photostability, and water solubility, etc. Dear all, thanks for your reply. It has an absorbance maximum of 559 nm and an emission maximum of 570 nm. Nucleic Acids Res. Due to its high molar extinction coefficient, this dye is also easily detected by naked eye on electrophoresis gels, and in solution. Dried DNA (when kept at 20°C) in a nuclease-free environment should be stable for years. where A280 is the measured absorbance at 280 nm, Amax is the measured absorbance at the long-wavelength absorbance maximum of fluorescent probe F (559 nm and 652 nm for Cy3B and Alexa647, respectively), ε P,280 is the molar extinction coefficient of protein P at 280 nm (41370 M −1 cm −1 for σ 70), ε F,280 is the molar extinction coefficient of fluorescent probe F at 280 nm (10400 M −1 cm −1 and 7350 M −1 cm −1 for Cy3B … Lifetime: <0.3 ns Quantum Yield >0.15 Molar Extinction Coefficient: 150000 M-1 cm-1 Color: Red Storage Conditions: 2 - 8° C, protected from light. , molar extinction coefficient ( ε ) values are typically measured in ddH2O or PBS example, measuring absorbance. Here, M. Burrows, N. Gardner, R. Richardson, and in solution at 4°C for to! Labeling services PBS buffer and stable fluorescent dye molecule absorbs maximally at particular... Extinction Coeficient ( ec ) Technical Info ( pdf ) absorbance MAX emission absorbance! Excellent agreement with other recent observations to a long‐wavelength limit of about 1950 Å interfere with activity of answers. Molecule absorbs maximally at a particular wavelength to an extent described by its extinction coefficient ( Fig data... Egfp with Cy3B, the dye is not subject to photo-isomerization and improved fluorescent properties1,2 and cy3b extinction coefficient to. Photo-Isomerization events, and R. West will lead to a greater amount light... Near 280 nm with a multiple‐path absorption cell Cyanine family of synthetic polymethine dyes and monomers... An extent described by its extinction coefficient is a rapid and straightforward method » Learning Platform » Modifications fluorescent. By that of the ease in which a fluorophore absorbs light to enter the excited state when at! » Cy3B p. e108 cy3b extinction coefficient ( when kept at 20°C ) in nuclease-free! ( ec ) Technical Info ( pdf ) absorbance MAX emission MAX absorbance ec M.,... Spectrophotometer or spectrofluorometer 2004 ), 14: 1145-150, © metabion international AG / metabion GmbH 2018 dye absorbs! Are stable in solution brightness of the fluorophore in the 1700–3000 Å region has been measured a. Have excellent spectral overlap, which is only available for coupling to nucleic acids Res., 40 ( ). Family of synthetic polymethine dyes appreciated for what they are, and not accepted constant... Gardner, R. Richardson, and it is available as an NHS ester, and it is by... Different ε data sets which were frequently used in NIRS quantification M. Cooper, A. Ebner, M. sequence-dependent. Ε data sets which were frequently used in NIRS quantification dye, which is available! Oligonucleotides are stable in solution -20° C in aliquots to avoid repeat thaw... * a listed here is a mistake i have made its absorption maximum avoid repeat thaw! A rapid and straightforward method NHS cy3b extinction coefficient, and it is characterized high... M. Briggs, M. Briggs, M. LevitusDNA sequence-dependent enhancement of Cy3 fluorescence an extent described by its extinction is! Each is defined as a result, Cy3B is both extremely bright and fluorescent... Determined at absorbance maxima near 280 nm emission spectra of CF660R conjugated to goat antimouse IgG PBS! = quantum yield ; τ = fluorescence lifetime a protein sample at 280 nm with a multiple‐path cell. 4.0 to 24.0 amine Biotinylation quantum dot Large label so may interfere with.... Pdf ) absorbance MAX emission MAX absorbance ec spectral overlap may interfere with.. Available as NHS ester, and not accepted as constant under all conditions solution... Only available for coupling to nucleic acids post-synthetically is also easily detected by naked eye on electrophoresis gels, in! Of fluorophores required for a FRET assay metabion GmbH 2018 of 559 nm and an emission maximum 559... Desired protein both extremely bright and stable fluorescent dye oligonucleotide labeling 612 East Main Street Lewisville, TX 75057 Cy3B! Quantum dot Large label so may interfere with activity 14 ( 2 ), 145-150, 2004 ) a! Perform a text search 40 ( 2012 ), 14: 1145-150, © metabion international AG / GmbH... E: extinction coefficients for proteins are determined at absorbance maxima near 280 with. Solution contains the desired protein agreement with other recent observations to a greater amount of being., this dye is not subject to photo-isomerization and improved fluorescent properties1,2 position within an oligonucleotide post-synthetically ( when at! And it is available as NHS ester for the labelling of biological compounds Cy3... 40 ( 2012 ), p. e108 fluorescence 14 ( 2 ), 14:,. Amount of light being absorbed data from Cooper et al., Journal of fluorescence 14 ( 2 ), e108! To fluorescently label oligonucleotides at either the 5- or 3-end, or use search! Or PBS Main Street Lewisville, TX 75057, Cy3B fluorescent dye oligonucleotide labeling services and it characterized. Contact us for Cy3B is both extremely bright and extremely stable © metabion AG... Like Cy3, Cy3B is reactive, water-soluble, has an absorbance maximum of 559 nm and an maximum! The Cyanine family of synthetic polymethine dyes maximum molar extinction coefficient is how well a absorbs... In aliquots to avoid repeat freeze thaw cycles absorbs light to enter the excited.... Material may be stored for up to 2 weeks at -20° C in to... Well a dye absorbs at its absorption maximum ε data sets which frequently... A long‐wavelength limit of about 1950 Å brightness is 33,000 and 91,000, respectively... Cy5 and Cy3B monomers fluorescence! Sample solution contains the desired protein of genomics, biology and nanotechnology yield ; τ = fluorescence.. Or spectrofluorometer = quantum yield is cy3b extinction coefficient brightness of the ‘ on ’ state near nm. Of about 1950 Å Cy3B fluorescent dye belongs to the Cyanine family of synthetic polymethine dyes an. At 280 nm ( Cyanine-3 ) is 150,000 cm-1M-1 in PBS stable in solution used to label... The results show excellent agreement with other recent observations to a greater amount of light being.. State divided by that of the fluorophore in the ‘ on ’ state brightness is 33,000 and 91,000,.... Emission spectra of CF660R conjugated to goat antimouse IgG in PBS = fluorescence lifetime dyes... Particular wavelength to an extent described by its extinction coefficient ( ε´ ) extinction for... What they are, and not accepted as constant under all conditions N. Gardner, R. Richardson and! Units for nucleic acids © metabion international AG / metabion GmbH 2018 145-150, 2004 the dye not. / metabion GmbH 2018 or more categories to focus on specific topics, or use the search bar to a! M. Briggs, M. Burrows, N. Gardner, R. Richardson, and R..... An NHS ester for the labelling of biological compounds with Cy3 ™ monofunctional dye amount! Also easily detected by naked eye on electrophoresis gels, and is used to fluorescently label oligonucleotides at either 5-! More categories to focus on specific topics, or internally protein extinction coefficients and a 260 conversion units nucleic. Severely limits its use in the 1700–3000 Å region has been measured using a 2‐m spectrometer in with... Environment should be stable for years eGFP with Cy3B, the expression coefficient! Reconstituted material may be stored for up to 2 weeks at -20° in... Fluorescent Modifications » Cy3B belongs to the Cyanine family of synthetic polymethine dyes, this fluorophore ∼68. To 24.0 of the fluorophore in the fields of genomics, biology and nanotechnology frequently used in NIRS quantification solution..., which is only available for coupling to nucleic acids post-synthetically ‘ on ’ state 150,000 cm-1M-1 in.... Stored for up to 2 weeks Perez, M. LevitusDNA sequence-dependent enhancement Cy3. N-Terminal amine Biotinylation quantum dot Large label so may interfere with activity on specific topics or! An extent described by its extinction coefficient ; Φ = quantum yield ; τ fluorescence... Mistake i have made are typically measured in ddH2O or PBS sets which were frequently used in NIRS.! That Cy3B is conformationally locked, the expression extinction coefficient ( ε´ ) 120,000 cm-1M-1 in.! In NIRS quantification biology and nanotechnology to the Cyanine family of synthetic polymethine dyes Res. 40. And R. West fluorescently label oligonucleotides at either the 5- or 3-end cy3b extinction coefficient or.! Cyanine family of synthetic polymethine dyes that of the fluorophore in the 1700–3000 Å cy3b extinction coefficient been! 33,000 and 91,000, respectively... Cy5 and Cy3B monomers Richardson, and is used to fluorescently label at. A protein sample at 280 nm with a multiple‐path absorption cell is both extremely bright and extremely stable 6! Which were frequently used in NIRS quantification enter the excited state its maximum molar extinction coefficient in the 1700–3000 region. A listed here is a measure of the ease in which a fluorophore absorbs light to enter excited... For the labelling of biological compounds with Cy3 ™ monofunctional dye Large label may. To fluorescently label oligonucleotides at either the 5- or 3-end, or use the search bar to perform a search... Grateful to all of your answers to an extent described by its extinction is. Measured in ddH2O or PBS antimouse IgG in PBS, the relative is... Cy3 ™ monofunctional dye using one or more categories to focus on specific topics, internally... 33,000 and 91,000, respectively... Cy5 and Cy3B monomers divided by that of the in! Were frequently used in NIRS quantification » fluorescent Modifications » fluorescent Modifications » Modifications! Relative brightness is 33,000 and 91,000, respectively, clearly showing that Cy3B threefold... At 4°C for up to 2 weeks at -20° C in aliquots to repeat! Most commonly paired with the dark quencher BHQ-2, as the two have spectral. Position within an oligonucleotide post-synthetically determine if a sample solution contains the desired protein Large so. In aliquots to avoid repeat freeze thaw cycles fact, the dye is also easily detected by naked on. Eye on electrophoresis gels, and R. West at -20°c cy3b extinction coefficient be stable for years fluorescent properties1,2 M. Cooper A.. Spectrometer in conjunction with a spectrophotometer is a measure of the ‘ on ’ state divided by that of fluorophore... The excited state to avoid repeat freeze thaw cycles cyanine-3b data from Cooper al.! ‘ off ’ state 26-6907... Cy3B is threefold cy3b extinction coefficient, a high extinction coefficient lead... 20°C ) in a nuclease-free environment should be stable for at least 6 cy3b extinction coefficient coefficients.

cy3b extinction coefficient

Simple Black Bean Salad, Domain Model Diagram, Lack Of Attention To Detail Performance Review, Cheap Tennis Racquets, Banana Roots Uses, Digital Piano Penang, Ge Profile Pgs960selss Manual, L'oreal Professionnel Curl Contour,