AMC (7-Amino-4-methyl-coumarin)

UV-excitable dye, used in enzyme assays using cuvettes or flow cytometry.

Cy3, Cy5 are dyes with extremely high extinction coefficients and fluorescence. Thus, they are especially suitable for very sensitive localization assays of peptides in cells. Their disadvantage is the high instability of the molecules under peptide synthesis conditions. Therefore the yields are comparatively low.

Dabcyl is a non-fluorescent dye predominantly used as a quencher for other fluorophores (esp. Fluorescent type dyes, EDANS.). If Dabcyl is coupled to a peptide in close proximity to a fluorophore, it absorbs the emitted light of the fluorophore. Enlarging this distance (i.e. by enzymatic cleavage of the peptide) results in excitation of the fluorophore with an emission signal that can be detected.

Dansyl is also used as a fluorophore quencher. Unlike Dabcyl, it inherits own fluorescence and thus might not be as useful for highly sensitive assays

2,4-Dinitropheny is a non-fluorescent dye that can be used as a fluorophore quencher (see Dabcyl for more details).

DNP-Lysineis a non-fluorescent dye that can be used as a fluorophore quencher, for custom peptide (see Dabcyl for more details).

EDANS is a commonly used dye in FRET (fluorescence resonance energy transfer) peptides in combination with Dabcyl as quencher.

Fluorescent is the commonly used fluorescent dye in confocal laser-scanning microscopy and flow cytometry applications.

NBD is a fluorescent dye, used for amine modification.

p-Nitro-Aniline is a chromogen used as colorimetric enzyme substrate in many standard enzyme assays in cuvettes.

Rhodamine B represents one among a numerous range of rhodamine dyes, used in fluorescent peptide assays.

FRET stands for fluorescence resonance energy transfer, or Förster resonance energy transfer. FRET is a mechanism describing excited state energy transfer from the initially excited donor to an acceptor. The donor molecules typically emit at shorter wavelengths that overlap with the absorption of acceptors. The process is a distance-dependent interaction between the electronic excited states of two molecules without emission of a photon.

FRET can be used for conformational investigation of peptide folding. FRET peptides are widely used as suitable substrates in enzyme studies, such as:

Functional characterization of peptidases / proteases / kinases / phosphatases
Kinetic characterization of peptidases / proteases / kinases / phosphatases
Screening and detection of new proteolytic enzyme

A quencher is very efficient at absorbing certain wavelengths. When near a dye that emits at the absorbed wavelength, the light is “quenched”, and no longer visible. Quenchers are very similar in structure to dyes. The difference is that they emit in undetectable ranges, or in undetectable amounts. The ability to quench is a function of distance from the dye in most cases. Molecular beacons are effective in that the quencher actually comes in contact with the dye. Different quenchers are best for different dyes.

Yes. Use the succinimidyl ester version of the dye and conjugate it to either a N-terminal and Lysine side-chain amino linker. Other options include using a Lys-FAM or Lys-TAMRA for Solid Phase Peptide Synthesis. These dyes are already conjugated to the Lys side-chain amino linker.

Both 5-FAM (5-carboxyfluorescein, single isomer) and FITC (fluorescein-5-isothiocyanate, isomers) are forms of the fluorescent dye fluorescein. FITC refers to a particular form of reactive species, the isothiocyanate, of the dye. It yields a urea linkage upon reaction with a primary amine. 5-FAM is the preferred reagent for labeling a protein or peptide. It results in an amide bond when reacted with a primary amine. The chemistry is more robust and better yielding. Furthermore, it has been shown that 5-FAM is less susceptible to photo-bleaching. The 5-FAM and FITC conjugated protein and peptide have similar spectral properties.

Yes. Tell us the dye or modification you are looking to use; we will find out if it is commercially available. If it is not, there is a possibility we can make it in-house. If neither of these is an option we will do our best to see if there is another dye or modification that can give you similar results. If any of these options work for you, we will then send you a quotation.

Spectra data can be found (click here). These values are provided by the manufacturer of the fluorescent dye and are generally calculated from the free dye not attached to a protein or peptide. As a general rule, these values work fine for the common protein or peptide user as there is little change, if any at all, when the dye is attached to a protein or peptide. The particular base composition of a protein or peptide can play a role as can pH in many cases, particular fluorescein and related dyes.

The answer is complicated in that there are many ways to place different conjugations on a peptide, but we are still limited by what is available to us for conjugation and compatibility issues. The easiest way is if one or both of the conjugates are available as thiol of cysteine and/or support bound reagents. If at least one reagent is available, the other conjugate can often be attached through a primary amine at the other end of the peptide. Chemical compatibility is avoided in this case. If neither conjugate is available as a thiol of cysteine or support bound reagent, then we often will use an orthogonal linker scheme incorporating both a thiol linker and an amino linker. This requires that one of the conjugates is available as a maleimide, which is thiol specific under neutral pH conditions. Most of all the commonly used dyes are available in both the succinimidyl and maleimidyl ester forms. The most common, such as fluorescein, TET, HEX, TAMRA, Cy™5 and Cy3 are also available as primary amine or support bound reagents. We will help you design your specific peptide when you place your order. Also, see our Products section on dyes for more information on what is available.

Left: Conventional cyclization
Right: Backbone cyclization with all possible connections to backbone amides

Biotin (or vitamin H) is a small biologically active molecule with a molecular weight of 244.31 Da. It acts as a co-enzyme in living cells. With its highly specific affinity towards streptavidin, it is used in various biotechnology assays &peptide synthesis for quality and quantity testing.

Desthiobiotin: Binds to streptavidin but can be displaced by biotin. Useful when you need to get your peptide out of a binding experiment. THE molecular weight: 214.31 Da.

Farnesyl is a potential substrate to study demethylase activity in enzyme assays.

Phosphorylationof Ser, Thr and Tyr is one of the more common modifications of amino acids in nature. Many hormones can adapt the activity of specific enzymes by increasing their phosphorylation state of Ser or Thr residues. Growth factors (like insulin) can trigger phosphorylation of Tyr.

The phosphate groups on these amino acids can be quickly removed, thus Ser, Thr and Tyr function as molecular switches during regulation of cellular processes (e.g. cancer proliferation).

Sulfurylation at Ser, Thr and Tyr is another Peptide Modification of amino acids in nature. Activity of many enzymes depends on the oxidation state of SH-groups in these residues.