Fluorescent- and biotin-labeled peptides are invaluable tools for biochemistry, having numerous applications in enzymology, protein chemistry, immunology and histochemistry. Novabiochem® range offers one of the most extensive ranges of labeling reagents for the synthesis of such peptides, including the unique NovaTag™ resins for the production of C-terminally-labeled peptides.


The spectral properties of Novabiochem®’s chromogenic and fluorogenic derivatives are summarized in Table 1.

One of the most important applications of such reagents is in the synthesis of fluorescence-quenched enzyme substrates. These are highly sensitive tools for probing protease specificity and activity, particularly for endoproteases where conventional carboxy-terminally labeled substrates are not always appropriate. Such substrates typically contain a fluorophore and a quencher group attached to either side of the cleavage site. In the intact molecule, the natural fluorescence of the fluorophore is suppressed by the proximity of the quencher through a process called fluorescence resonance energy transfer (FRET). Upon cleavage of the substrate by a protease, the quencher and fluorophore become separated, leading to an increase in fluorescence, which can then be detected spectrophotometrically (Figure 1). Sensitivity is determined primarily by the distance between fluorophore and quencher, which should be in the range 10-100 Å, and the extent of overlap between the absorbance spectrum of the quencher and the emission spectrum of the fluorophore. The recommended fluorophore-quencher pairs are listed in Table 1.

Table 1: Spectral properties of Novabiochem range of dyes.

NovaTag™ resins


Figure 1. Fluorescence-quenched peptide substrate


Figure 2. NovaTag™ resins

Labels are most frequently incorporated at the N-terminus of the peptide during solid phase synthesis as this is synthetically very straightforward using carboxylic acid derivatives of labels such as biotin-OSu, TAMRA, etc. For many applications, however, it is advantageous to place the label at the C-terminus, particularly if the N-terminus is required for biological activity, or if the peptide contains more than one label.

Furthermore, for FRET-based enzyme substrates, it is often preferable to place the fluorophore/quencher pair at the N- and C-termini, rather than on amino-acid side chains as this avoids modification of the native peptide sequence.

Novabiochem®’s NovaTag™ resins are unique tools designed to streamline the Fmoc SPPS of chromogen and biotin labeled peptides1. Each resin contains a standard TFA-cleavable linker which has been modified to incorporate a diamine spacer that is either orthogonally protected or pre-derivatized with a chromogenic label (Figure 2). This arrangement allows C-terminally labeled peptides to be prepared quickly and efficiently with the minimum number of synthetic steps. Pre-loaded resins are available which on cleavage directly provide peptides containing fluorophores (Dansyl, Mca, EDANS) and quencher groups (Dnp) for FRET applications, or affinity labels (biotin, biotin-PEG, hydroxylamine) for bioconjugation and surface immobilization.

The pre-loaded resins are easy to use and can be generally employed in automated instrumentation without modification of existing Fmoc synthesis protocols. The only exceptions are the EDANS NovaTag™ and Universal NovaTag™ resins where attachment of the first residue must be carried out under modified conditions as this involves acylation of a secondary amine (Method 2). Following chain extension and cleavage with TFA in the usual manner, products are obtained containing the appropriate fluorophore or biotin at the C-terminus.

The use of pre-loaded resins avoids the inherent problems of poor solubility and inefficient coupling, as well as the additional steps and costs, that are associated with the introduction of biotin and certain fluorophores in solid phase synthesis. The approach is particularly suited to the production of peptides for high-throughput screening, as it removes the difficulty of ensuring complete label incorporation for all molecules in the array. NovaTag™ resins incorporating different labels and spacer groups can also be custom manufactured.

Universal PEG NovaTag™ resin


For situations where it is not always apparent at the outset which is the optimum label or combination of labels for a given application, Novabiochem® offers the Universal NovaTag™ resins. These supports facilitate the synthesis of peptides bearing any number of different acyl moieties at N- and C-termini from a single solid phase synthesis (Figure 3). Universal resins are also useful for preparing labeled peptides containing fluorophores that are not compatible with Fmoc SPPS protocols, such as TAMRA and FAM2, since they allow the labels to be easily introduced as the final step before cleavage. Universal PEG NovaTag™ resin is particularly efficacious for applications where a hydrophilic spacer is required between the peptide and the label and where the peptide solubility is an issue.


Figure 3.Synthesis using Universal NovaTag™ resin

After loading (Method 2) of the first amino acid to the resin-bound secondary amine, chain extension is carried out under standard Fmoc methods. Following synthesis, the resin can be partitioned and each aliquot end-capped with the appropriate carboxyl-functionalized label. The pendant Mmt group is then removed using HOBt/TFE/DCM (Method 1) and the C-terminal label introduced to each resin aliquot. Thus, from a single synthesis any number of label variations for a given sequence can be prepared.

Universal PEG NovaTag™ resin has been used to prepare fluorescently-labled Shc Src homology 2 domain-binding peptides linked to cell penetrating sequences via a PEG spacer3 and dimeric SMAC PEG-linked peptides4. Universal NovaTag™ resin has been utilized to prepare peptides C-terminally modified to ketone for ligation5.

Method 1: Removal of Mmt group

  1. Add 0.6 M HOBt in DCM/TFE (1:1) to resin swollen in DCM.
  2. Gently agitate for 1h; solution goes dark red.
  3. The solvent is removed by filtration, and steps 1 & 2 are repeated.
  4. The resin is removed by filtration, washed with DMF and used immediately in synthesis, or washed further with DCM and then MeOH, dried and stored for later use.

NovaTag™ Resins

Reagents for introduction of optical labels



Fmoc-Asp(Wang resin)-AMC


Fmoc-Lys(carbamate Wang resin)-AMC

Enzyme substrates based on the 7-amino-4-methylcoumarin (AMC) fluorophore are very popular tools for studying protease activity and specificity6. In such substrates, the AMC is typically linked to the peptide through formation of an amide bond between the coumarin amine and the carboxyl group of the C-terminal amino-acid residue (Figure 4). Proteolysis of this amide bond liberates free AMC, resulting in a large increase in fluorescence that can be detected at 441 nm upon excitation at 342 nm.


Figure 4. Principle of AMC-labeled fluorogenic substrates.

The synthesis of peptide-AMC derivatives is particularly problematic owing to the poor nucleophilicity of the AMC amine group. The usual strategy involves first formation of the AMC derivative of the C-terminal amino-acid residue followed by fragment condensation or stepwise elongation. This approach is obviously not amenable to solid phase methods and cannot be applied to the production of enzyme substrate libraries for protease profiling. To overcome these limitations, we have introduced pre-loaded with amino acid-AMC derivatives: Fmoc-Asp(Wang resin)-AMC; Fmoc-Lys(carbamate Wang resin)-AMC. Aspartic acid and lysine were selected as these amino acids occur at the P1 position of endogenous substrates for several important proteases.

These resins are extremely simple to use and are fully compatible with standard Fmoc SPPS protocols. The free amine group can be acylated with Fmoc amino acids activated with PyBOP® or TBTU. Following peptide assembly, cleavage with 95% TFA releases the peptide-AMC directly from the solid support without any additional steps.

synthesis-using-universal -novatag

Figure 5. Synthesis of Ac-Asp-Glu-Val-Asp-AMC using Fmoc-Asp(Wang resin)-AMCSynthesis of Ac-Asp-Glu-Val-Asp-AMC using Fmoc-Asp(Wang resin)-AMC

7-Methoxycoumarin (Mca)






Mca NovaTag™ resin

The 7-methoxycoumarin group (Mca) fluoresces at 393 nm when stimulated at 328 nm, and is most commonly used in conjunction with 2,4-dinitrophenyl (Dnp) quenching groups7. It can be coupled on solid phase to free amines using Mca-OSu, Mca-OH, or incorporated during chain extension using a pre-formed building block such as Fmoc-Lys(Mca)-OH8. Fmoc-Lys(Mca)-OH and Mca-OH can be coupled using any standard coupling method, such as PyBOP®/DIPEA and DIPCDI/HOBt, whereas the preactivated derivative, Mca-OSu, couples best in DMSO or NMP in the presence of HOBt. The coumarin moiety is stable to the standard conditions employed in Fmoc SPPS.

Mca NovaTag™ resin provides peptides C-terminally modified with the Mca fluorophore attached via an ethylene diamine spacer1. Following removal of the Fmoc group, the resin-bound primary amine can be loaded with the first amino acid residue using standard activation methods, such as PyBOP, HOBt/DIPCDI. After peptide assembly, treatment with 95% TFA cleaves the Mca peptide directly from the resin.






Dabcyl is one of the most frequently utilized quenching groups because of its lack of innate fluorescence and spectral overlap (λmax 453 nm) with a number of commonly-used fluorophores, such as EDANS, Mca, TET, JOE, FAM. In the preparation of fluorescence-quenched peptide substrates, it is most frequently used in conjunction with EDANS as this pairing is particularly efficacious owing to their excellent spectral overlap9,10.

The Dabcyl group is most conveniently introduced during solid phase synthesis of the substrate. Addition to the N-terminal amino group is best achieved using Dabcyl-OSu in DMSO or NMP in the presence of HOBt. When the Dabcyl group is to be located in the peptide chain, the simplest approach is to introduce Lys(Dabcyl) at the desired position using Fmoc-Lys(Dabcyl)-OH activated with PyBOP®/DIPEA.

2,4-Dinitrophenyl (Dnp)



The Dnp group (λmax 348 nm) is the preferred quenching group for the Mca fluorophore7. It is most easily incorporated into a peptide as Fmoc-Lys(Dnp)-OH, which can be coupled using any standard activation method.


Dnp NovaTag™ resin

This resin is ideal for the assembly of labeled peptides incorporating a C-terminal Dnp group1. Following removal of the Fmoc group, the resin-bound primary amine can be loaded with the first amino acid residue using standard activation methods, such as PyBOP®, HOBt/DIPCDI. After peptide assembly, treatment with 95% TFA cleaves the Dnp peptide directly from the resin. This resin is particularly advantageous for the synthesis of FRET peptides, since the presence of the quencher in every peptide chain minimizes the levels of fluorescent unquenched by-products and so reduces background fluorescence of the product FRET substrates.


Fmoc-Asp(EDANS)-OH and Fmoc-Glu(EDANS)-OH

The EDANS/Dabcyl fluorophore-quencher pair is one of the most commonly-used for FRET applications, owing to excellent spectral overlap between the emission spectrum of EDANS (λex 341 nm, λem 471 nm) and absorbance spectrum of Dabcyl (λmax 453 nm)9,10 (Figure 6). Quenching of the fluorescence of EDANS by Dabcyl is consequently highly efficient, with up to 40-fold enhancements in fluorescence having been observed upon proteolysis of Dabcyl/EDANS-labeled peptides11.


Figure 6. Absorbance and emission spectra of Dabcyl and EDANS7.

To incorporate EDANS within the peptide chain, the simplest approach is to use either Fmoc-Asp(EDANS)-OH or Fmoc-Glu(EDANS)-OH during peptide assembly11, 12. Introduction of these derivatives during SPPS can be achieved using PyBOP®/DIPEA activation in conjunction with an extended coupling time12. Powerful acylating reagents such as PyBrOP should be avoided as their use may lead to acylation of the naphthylamine nitrogen.

EDANS NovaTag™ resin

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