Cyanines are formally compounds with two nitrogen atoms linked by an odd number of methene units. 26 – 28. The nitrogen atoms are parts of the heterocyclic units (such as indole, benzoxazol, or benzothiazol).
What are cyanine dyes used for?
Cyanine dyes are used to label proteins, antibodies, peptides, nucleic acid probes, and any kind of other biomolecules to be used in a variety of fluorescence detection techniques (Ünlü et al., 1997; Osterman et al., 2013) [5,6].
What is FAM fluorophore?
A single isomer derivative of fluorescein. FAM is the most commonly used fluorescent dye attachment for oligonucleotides and is compatible with most fluorescence detection equipment. It becomes protonated and has decreased fluorescence below pH 7; it is typically used in the pH range 7.5–8.5.
What does Cy5 stand for?
Cy5. 5 is a near-infrared (IR) fluorescence-emitting dye (excitation/emission maximum 678/694 nm). Cy7 is a near-IR fluor that is invisible to the naked eye (excitation/emission maximum 750/776 nm). It is used in in vivo imaging applications, as well as the Cy7. 5 dye.
What is Cyanine Blue?
1a : a strong blue that is greener and deeper than Sèvres and redder and darker than cerulean blue (see cerulean blue sense 1b) — called also Leitch’s blue.
How do you choose a fluorophore?
Select fluorophores with high extinction coefficients ( ε ) One defining factor of a fluorophore’s brightness is its extinction coefficient (a measurement of the probability of absorbing a photon of light); the higher the value of the extinction coefficient the brighter the fluorophore.
What is a polymethine chain?
: any of a class of dyes (as cyanines or merocyanines) characterized by a resonance structure containing a conjugated chain of carbon atoms that is at least in part an open chain [as in −CH(=CH−CH)n=] attached to two polar atoms (as two amino nitrogen atoms either one of which is considered to be positively charged)
What is Rox in qPCR?
ROX, also known as carboxyrhodamine, is an inert fluorescent dye that can be added to the qPCR master mix. Unlike reporter dyes in qPCR (e.g. SYBR Green), ROX is referred to as a passive dye, since its fluorescence signal is not influenced by the PCR reactions.
What is HEX fluorophore?
HEX is a fluorescent compound with an excitation peak at 533 nm and an emission peak at 559 nm. It can be excited using a 532 nm laser paired with a 575/25 nm bandpass filter, a configuration that can be found, for example, in the BD Special Order LSRFortessa™ Cell Analyzer.
Is Tamra a quencher?
TAMRA dye is an effective quencher for fluorophores with emission maxima less than 560 nm. Dyes with longer wavelength emissions will not be effectively quenched by TAMRA. In addition, TAMRA has its own fluorescence which complicates data analysis due to crosstalk between the channels.
Is Cy5 far-red?
Invitrogen Cy5 dye is a bright, far-red-fluorescent dye with excitation ideally suited for the 633 nm or 647 nm laser lines.
Is Cy3 a fluorophore?
Cy®3 is an orange fluorophore commonly used in applications such as immunolabeling, nucleic acid labeling, fluorescence microscopy, and flow cytometry. The dye has an absorption wavelength that peaks around 548-552 nm, and an emission maximum around 562-570 nm.
What color is Cy3?
Cy3 dye dashboard The Cy3 dye is a traditional orange-fluorescent label for protein and nucleic acid conjugates used for imaging, flow cytometry, and genomic applications.
What wavelength is Tritc?
532 nm Tetramethylrhodamine (TRITC) is a bright orange-fluorescent dye with excitation ideally suited to the 532 nm laser line. It is commonly conjugated to antibodies and proteins for cellular imaging applications.
How does Alexa Fluor work?
Alexa Fluor dyes can be conjugated directly to primary antibodies or to secondary antibodies to amplify signal and sensitivity or other biomolecules. The excitation and emission spectra of the Alexa Fluor series cover the visible spectrum and extend into the infrared.
What does Texas red stain?
Texas Red or sulforhodamine 101 acid chloride is a red fluorescent dye, used in histology for staining cell specimens, for sorting cells with fluorescent-activated cell sorting machines, in fluorescence microscopy applications, and in immunohistochemistry.
Can I use FITC and PE together?
FITC overlap a lot with Pe, don’t use them together on same cells. PerCP-‐Cy5. 5 overlap surprisingly a lot with BV711, don’t use together.
How do you compensate FACS?
As a general rule, compensate with the fluorochromes from the far-red end of the spectrum (higher wavelength), step-wise down to those fluorochromes at the lower end of the spectrum (lower wavelength). Do not forget to check the compensation in all channels.
How do you choose a fluorophore for flow cytometry?
Expression of Common Markers. Knowing the relative expression of antigen markers can help you optimize your fluorophore selections in multicolor flow cytometry. In general, select bright fluorophores for your weakly expressed antigens and select dimmer fluorophores for highly expressed antigens.
Graduated from ENSAT (national agronomic school of Toulouse) in plant sciences in 2018, I pursued a CIFRE doctorate under contract with Sun’Agri and INRAE in Avignon between 2019 and 2022. My thesis aimed to study dynamic agrivoltaic systems, in my case in arboriculture. I love to write and share science related Stuff Here on my Website. I am currently continuing at Sun’Agri as an R&D engineer.