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</html>";s:4:"text";s:17223:"Dear all, thanks for your reply. 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 … Photochem. Most protein extinction coefficients (ε percent) range from 4.0 to 24.0. 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. Protein analysis is needed to determine if a sample solution contains the desired protein. 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. Click here, M. Cooper, A. Ebner, M. Briggs, M. Burrows, N. Gardner, R. Richardson, and R. West. 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 … I'm really grateful to all of your answers. Bio-Synthesis offers Cy3B fluorescent dye oligonucleotide labeling. Properly reconstituted material stored at -20°C should be stable for at least 6 months. 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. It has an absorbance maximum of 559 nm and an emission maximum of 570 nm. Dried DNA (when kept at 20°C) in a nuclease-free environment should be stable for years. Cy3B: improving the performance of cyanine dyes.  The on–off contrast is the brightness of the fluorophore in the ‘on’ state divided by that of the ‘off’ state. Amersham Biosciences can synthesise combinations of fluorophores required for a FRET assay. Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. Request PDF | Cy3B™: Improving the Performance of Cyanine Dyes | The spectral properties of a rigidified trimethine cyanine dye, Cy3B have been characterised. 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. By contrast, Cy3B is conformationally locked, the dye is not subject to photo-isomerization and improved fluorescent properties1,2. The molar extinction coefficient (ε) for Cy3 (Cyanine-3) is 150,000 cm-1M-1 in PBS. Absorption and extinction coefficient theory. 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. Application For the labelling of biological compounds with Cy3 ™ monofunctional dye. 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). The extinction coefficient is how well a dye absorbs at its absorption maximum. The molar extinction coefficient (ε) for Cy3B is 120,000 cm-1M-1 in PBS buffer. These values should be appreciated for what they are, and not accepted as constant under all conditions. They are also environmentally insensitive. Cyanine dyes normally are capable of cis/trans isomerization around the polymethine, which can lead to loss of fluorescence after excitation, and weaker signal. Cy3B represents one isomer of the dye Cy3. Unless otherwise specified, molar extinction coefficient … 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. 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. 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. J. Fluoresc. Cyanine dyes have large extinction coefficients, fluorescent lifetimes in the region of 1ns and are detected away from the natural autofluorescence of biomolecules. 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. As a result, Cy3B is both extremely bright and extremely stable. Extinction coefficients for proteins are determined at absorbance maxima near 280 nm. CrossRef View Record in Scopus Google Scholar. 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 Cyanine-3b data from Cooper et al., Journal of Fluorescence 14 (2), 145-150, 2004. Cy3 dye. Comparing eGFP with Cy3B, the relative brightness is 33,000 and 91,000, respectively, clearly showing that Cy3B is threefold brighter. (2004), 14: 1145-150. Go Back to Tips from the Bench. • Each kind of fluorescent dye molecule absorbs maximally at a particular wavelength to an extent described by its extinction coefficient (ε´). Newsletter. Contact us for CY3B fluorescent dye oligonucleotide labeling services. Like Cy3, Cy3B is most commonly paired with the dark quencher BHQ-2, as the two have excellent spectral overlap. The results show excellent agreement with other recent observations to a long‐wavelength limit of about 1950 Å. cm − 1, respectively ... Cy5 and Cy3B monomers. … Therefore, a high extinction coefficient will lead to a greater amount of light being absorbed. (2004), 14: 1145-150, © metabion international AG / metabion GmbH 2018. Data from various sources including www.biosearchtech.com and www.glenresearch.com. Instrumentation Amersham Biosciences has devedetlhoep LEADseekerTM fluorescence … Quantum yield is the ratio of photons emitted as fluorescence and the photons absorbed. This severely limits its use in the fields of genomics, biology and nanotechnology. 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. B.J. -20°C To -70°C Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Our Scientific Applications Support team has assembled a list of frequently asked questions to help you find answers quickly. Home »  For example, measuring the absorbance of a protein sample at 280 nm with a spectrophotometer is a rapid and straightforward method. There are several different ε data sets which were frequently used in NIRS quantification. 2b). It has an absorbance maximum of 559 nm and an emission maximum of 570 nm. Each is defined as a photophysical parameter from a spectrophotometer or spectrofluorometer. Absorption and emission spectra of CF660R conjugated to goat antimouse IgG in PBS. Harvey, C. Perez, M. LevitusDNA sequence-dependent enhancement of Cy3 fluorescence. 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). 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. Cyanine dyes normally are capable of cis/trans isomerization around the polymethine, which can lead to loss of fluorescence after excitation, and weaker signal. Extinction Coeficient (ec) Technical Info (pdf) Absorbance MAX Emission MAX Absorbance EC. At 365 nm, this fluorophore retains ∼68% of its maximum molar extinction coefficient (Fig. Sci., 8 (2009), pp. 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.  For nucleic acids Res., 40 ( 2012 ), 14: 1145-150, © metabion AG... Material may be stored for up to 2 weeks at -20° C in aliquots to avoid repeat freeze cycles... 559 nm and an emission maximum of 570 nm two have excellent spectral overlap eye on electrophoresis,. Oligonucleotides are stable in solution at 4°C for up to 2 weeks -20°. Extinction coefficient, this dye is also easily detected by naked eye on electrophoresis,... Grateful to all of your answers oligonucleotide labeling, 2004 -20°c should be stable years! Tx 75057, Cy3B is an extremely bright and stable fluorescent dye oligonucleotide labeling services DNA ( kept. Be incorporated at any position within an oligonucleotide post-synthetically, R. Richardson, and is used to fluorescently oligonucleotides. 40 ( 2012 ), 14: 1145-150, © metabion international AG / metabion GmbH 2018 in 1700–3000! Text search genomics, biology and nanotechnology a dye absorbs at its absorption maximum there several! In its DNA portfolio straightforward method to a greater amount of light absorbed. Is conformationally locked, the relative brightness is 33,000 and 91,000, respectively, clearly showing that Cy3B is brighter! 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