Peptide Resources
A peptide is acidic if the overall net charge of the peptide is negative. For an acidic peptide, if the total number of charges of the peptide at pH 7 is greater than 25% of the total number of residues, add a small amount of 0.1M ammonium bicarbonate to dissolve the peptide and dilute it with water to the desired concentration. Make certain that the resulting pH of the peptide solution is about 7 and adjust the pH as needed.
A peptide is basic if the overall net charge of the peptide is positive. For a basic peptide, if the total number of charges of the peptide at pH 7 is between 10-25% of the total number of residues, add a small amount of 25% acetic acid to dissolve the peptide and dilute it with water to the desired concentration.
A peptide is considered neutral if the overall net charge of the peptide is zero. If the total number of charges is greater than 25% of the total number of residues, use the strategy described in section 1. If the total number of charges is between 10-25% of the total number of residues, use organic solvents as recommended elsewhere in this document.
If the total number of charges of a peptide is less than 10% of the total number of residues, use of organic solvents is recommended.
Dissolve peptides in 0.1% aqueous acetic acid to yield a target concentration of 1-5 mg/mL. Use sonication if necessary.
Small amounts of dilute(10%) aqueous acetic acid for basic peptide antigen or aqueous ammonia for acidic peptides may help dissolution of these peptides.
If peptides are still insoluble, add acetonitrile up to 20%(v/v), and use sonication to help dissolution.
Lyophilize any remaining insoluble peptides to remove water, acetic acid and acetonitrile. When the peptides are completely dry, add neat DMF or DMSO (dropwise) until the peptides are dissolved. Slowly dilute the solution with water to desired concentration. If precipitation occurs during dilution, add more DMF or DMSO (dropwise) to dissolve the precipitate.
A peptide is acidic if the overall net charge of the peptide is negative. For an acidic peptide, if the total number of charges of the peptide at pH 7 is greater than 25% of the total number of residues, add a small amount of 0.1M ammonium bicarbonate to dissolve the peptide and dilute it with water to the desired concentration. Make certain that the resulting pH of the peptide solution is about 7 and adjust the pH as needed.
A peptide is basic if the overall net charge of the peptide is positive. For a basic peptide, if the total number of charges of the peptide at pH 7 is between 10-25% of the total number of residues, add a small amount of 25% acetic acid to dissolve the peptide and dilute it with water to the desired concentration.
A peptide is considered neutral if the overall net charge of the peptide is zero. If the total number of charges is greater than 25% of the total number of residues, use the strategy described in section 1. If the total number of charges is between 10-25% of the total number of residues, use organic solvents as recommended elsewhere in this document.
If the total number of charges of a peptide is less than 10% of the total number of residues, use of organic solvents is recommended.
Lyophilized peptides are stable at room temperature for weeks. Upon arrival, always store lyophilized peptides in a freezer at – 20°C for maximum stability. For short-term storage, it is recommended to store peptides at 4°C.
Lyophilized peptides are often hydroscopic. For best results, maintain product for synthetic peptide in a dry environment. When preparing peptides for use or peptide antigen design for example, allow to equilibrate to room temperature before opening the container, reseal the vial quickly after weighing out desired quantity.
Assign a value of -1 to each acidic residue (D, E, and C-terminal COOH)
Assign a value of +1 to each basic residue (K, R and the N-terminal NH2)
Assign a value of +1 to each H residue at pH<6 and zero at pH >6.
Count the total number of charges of the peptide at pH 7 (all D, E, K, R, C-terminal COOH, and C-terminal NH2).
Calculate the overall net charge of the peptide
Hydrolysis
Peptides containing Asp (D)
Sequence contains Asp-Pro (D-P)
Similarly, if Asp-Gly (D-G) is present in the sequence
Sequences containing Ser (S)
Deamidation sequences containing:
Asn-Gly (N-G)
Gln-Gly (Q-G)
Asp-Gly (D-G)
Oxidation
The Cys (C) and Met (M)
Diketopiperazine and pyroglutamic acid formation
Gly (G) is in the third position from the N-terminus
Pro (P) or Gly (G) is in position 1 or 2
KLH, BSA, OVA Conjugates
Peptide-protein conjugates are used for custom antibody production against peptides. Peptides alone are mostly too small to elicit a sufficient immune response, so carrier proteins containing many epitopes help to stimulate T-helper cells, which help induce the B-cell response. It is important to remember that the immune system reacts to the peptide-protein conjugate as a whole so there will always be a portion of antibodies to the peptide synthesis, the linker and the carrier protein.
Among the most common carrier proteins one can find:
KLH (Keyhole Limpet Hemocyanin), a copper containing, non-heme protein found in arthropods and mollusca. It is isolated from Megathura crenulata and has a MW of 4.5 x 105 ~ 1.3 x 107 Da. KLH is the most commonly selected carrier due to its higher immunogenicity compared to BSA.
BSA (Bovine Serum Albumin), a plasma protein in cattle, belonging to the most stable and soluble albumins. It has a MW of 67 x 103 Da containing 59 lysines. About 30-35 of these primary amines are accessible for linker conjugation, which makes BSA a popular carrier protein for weak antigenic compounds. A disadvantage of BSA is that it is used in many experiments as a blocking buffer reagent. If antisera against peptide-BSA conjugates are used in such assays, false positives can occur, because these sera also contain antibodies to BSA.
OVA (Ovalbumin), a protein isolated from hen egg whites, with a MW of 45 x 103 Da. It is a good choice as second carrier protein to verify if antibodies are specific for the peptide alone and not the carrier protein (e.g. BSA).
MAPs (Multiple peptide antigen)
MAPs are branched peptides that can be used for direct immunization to produce antibodies. MAPs are usually big enough to raise the immune response.
The antigenic peptide of interest is being synthesized directly on the branched MAP structure. MAPs are available as MAP 4 (4 branches) or MAP 8 (8 branches) molecules:
Schematic graph of a MAP 8 and a peptide-protein conjugate:
AMC (7-Amino-4-methyl-coumarin)
UV-excitable dye, used in enzyme assays using cuvettes or flow cytometry.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
AMC 353 nm 422 nm 19.000

Cy3, Cy5
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.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
Cy™3 550 nm 570 nm 150.000
Cy™5 650 nm 670 nm 250.000

Dabcyl
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.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
Dabcyl 453 nm none 32.000

Dansyl
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
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
Dansyl 335 nm 526 nm 4.600

2,4-Dinitrophenyl (DNP)
2,4-Dinitropheny is a non-fluorescent dye that can be used as a fluorophore quencher (see Dabcyl for more details).
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
DNP 348 nm none 18.000

DNP-Lysine
DNP-Lysineis a non-fluorescent dye that can be used as a fluorophore quencher, for custom peptide (see Dabcyl for more details).
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
DNP-Lysine 348 nm none 18.000

EDANS (5-((2-aminoethyl)amino)napthalene-1-sulfonic acid)
EDANS is a commonly used dye in FRET (fluorescence resonance energy transfer) peptides in combination with Dabcyl as quencher.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
EDANS 335 nm 493 nm 5.900

Fluorescent
Fluorescent is the commonly used fluorescent dye in confocal laser-scanning microscopy and flow cytometry applications.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
Fluorescent 495 nm 520 nm 83.000

NBD (7-nitrobenz-2-oxa-1, 3-diazole)
NBD is a fluorescent dye, used for amine modification.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
NBD 486 nm 543 nm 27.000

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

Rhodamine B
Rhodamine B represents one among a numerous range of rhodamine dyes, used in fluorescent peptide assays.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
Rhodamine 550 nm 580 nm 90.000
Tamra
Tamra is the most commonly used rhodamine dye in fluorescence assays.
Dye Excitation maximum Emission maximum Molar Extinction Coefficient
Tamra 544 nm 576 nm 90.000
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
Chromophore/Fluorophore – Quencher Pairs
Chromophore/Fluorophore Lambda max (nm) Lambda em (nm) Quencher
MAC 432 441 -
Dabcyl 453 - -
Dansyl 335 526 Dabcyl
Dnp 348 - -
EDANS 341 471 Dabcyl
Mca 328 393 Dnp
FAM 494 518 Dabcyl
TAMRA 555 580 -
Mca Dpa - -
How does a quencher work?
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.
Can a dye be conjugated to protein or peptide internally?
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.
What is the difference between a 5-FAM and FITC labeled protein and peptide?
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.
Can I use a dye or modification that is not listed here?
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.
What are the absorption max and emission max values for my fluorescent labeled protein or peptide?
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.
Can you make a peptide with two different dyes or other conjugate?
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.
Different modes of cyclization for peptides:
Left: Conventional cyclization
Right: Backbone cyclization with all possible connections to backbone amides
Biotin and Desthiobiotin
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
Farnesyl is a potential substrate to study demethylase activity in enzyme assays.
Formic acid (Formyl)
Myristic acid (Myristoyl)
Palmitic acid (Palmitoyl)
Stearic acid (Stearyl)
Phosphorylation Peptide Modification
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).
Succinic acid (Succinyl)
Sulfurylation
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.
2nd base
U C A G
1st base U UUU (Phe/F)Phenylalanine
UUC (Phe/F)Phenylalanine
UUA (Leu/L)Leucine
UUG (Leu/L)Leucine
UCU (Ser/S)Serine
UCC (Ser/S)Serine
UCA (Ser/S)Serine
UCG (Ser/S)Serine
UAU (Tyr/Y)Tyrosine
UAC (Tyr/Y)Tyrosine
UAA Ochre (Stop)
UAG Amber (Stop)
UGU (Cys/C)Cysteine
UGC (Cys/C)Cysteine
UGA Opal (Stop)
UGG (Trp/W)Tryptophan
C CUU (Leu/L)Leucine
CUC (Leu/L)Leucine
CUA (Leu/L)Leucine
CUG (Leu/L)Leucine
CCU (Pro/P)Proline
CCC (Pro/P)Proline
CCA (Pro/P)Proline
CCG (Pro/P)Proline
CAU (His/H)Histidine
CAC (His/H)Histidine
CAA (Gln/Q)Glutamine
CAG (Gln/Q)Glutamine
CGU (Arg/R)Arginine
CGC (Arg/R)Arginine
CGA (Arg/R)Arginine
CGG (Arg/R)Arginine
A AUU (Ile/I)Isoleucine
AUC (Ile/I)Isoleucine
AUA (Ile/I)Isoleucine
AUG (Met/M)Methionine, (Start)
ACU (Thr/T)Threonine
ACC (Thr/T)Threonine
ACA (Thr/T)Threonine
ACG (Thr/T)Threonine
AAU (Asn/N) Asparagine
AAC (Asn/N)Asparagine
AAA (Lys/K)Lysine
AAG (Lys/K)Lysine
AGU (Ser/S) Serine
AGC (Ser/S)Serine
AGA (Arg/R) Arginine
AGG (Arg/R)Arginine
G GUU (Val/V)Valine
GUC (Val/V)Valine
GUA (Val/V)Valine
GUG (Val/V)Valine
GCU (Ala/A)Alanine
GCC (Ala/A)Alanine
GCA (Ala/A)Alanine
GCG (Ala/A)Alanine
GAU (Asp/D)Aspartic acid
GAC (Asp/D)Aspartic acid
GAA (Glu/E)Glutamic acid
GAG (Glu/E)Glutamic acid
GGU (Gly/G)Glycine
GGC (Gly/G)Glycine
GGA (Gly/G)Glycine
GGG (Gly/G)Glycine

Reverse Codon Table
This table shows the 20 standard amino acids used in proteins, and the codons that code for each amino acid.
Ala A GCU, GCC, GCA, GCG Leu L UUA, UUG, CUU, CUC, CUA, CUG
Arg R CGU, CGC, CGA, CGG, AGA, AGG Lys K AAA, AAG
Asn N AAU, AAC Met M AUG
Asp D GAU, GAC Phe F UUU, UUC
Cys QC UGU, UGC Pro P CCU, CCC, CCA, CCG
Gln Q CAA, CAG Ser S UCU, UCC, UCA, UCG, AGU,AGC
Glu E GAA, GAG Thr T ACU, ACC, ACA, ACG
Gly G GGU, GGC, GGA, GGG Trp W UGG
His H CAU, CAC Tyr Y UAU, UAC
Ile I AUU, AUC, AUA Val V GUU, GUC, GUA, GUG
Start AUG Stop UAG, UGA, UAA
In general, a good peptide antigen has the following properties: protein surface location, flexible (usually loop) rather than helical structure, complicate and unique sequence, not a post-translational modification site or functional site (unless the antibody is intended to recognize such a site) and easy for synthesis. But the quantitative relationship between these properties and antigenic strength is not clear
Peptide antigen design is usually done by two different approaches: predicting peptide’s physical-chemistry properties or making prediction based on statistic results. Both approaches have their limitations. Physical chemistry properties such as peptide location in a protein or its secondary structure, particular turn, are difficult to be predicted with high degree of accuracy. This is because the problem themselves are parts of one of the most challenge areas of modern science —- protein folding. Another problem is that in most cases, an isolated peptide in solution can not maintain its native conformation found in the protein. This is the major reason that antigens designed based on known 3D structures are also often failed.
Although Cys residues are often added to peptides to enable crosslinking to a carrier protein, a peptide synthesized with many Cys residues present can be difficult to handle and may not lead to a useful antibody. Multiple Cys residues may lead to the formation of covalently linked aggregates. The Cys-rich regions of proteins may have some disulfide bonds. The linear peptide with reduced Cys would therefore not represent the protein itself, which would be more structurally constrained.
Most peptide antigen requested range in length from 12 to 20 residues and are relatively easy to synthesize. No Cys residues should be internal to the peptide sequence.
Fluorophores Absorption and Emission Data
The table lists the properties of the most commonly used fluorophore for peptide labeling of your interest in the life sciences. The fluorophores absorbance wavelength from 325nm to 743nm (from blue color to red color), the emission wavelength from 386nm to 770nm.
Fluorophore Dyes Ex (nm) Em (nm)
Hydroxycoumarin 325 386
Dansyl 340 578
7-Amino-4-methylcoumarin 351 430
methoxycoumarin 360 410
Alexa fluor 345 442
aminocoumarin 350 445
MAC 345 445
Dabcyl 453 -
Cy2 490 510
FAM 495 517
Alexa fluor 488 494 517
Fluorescein FITC 495 519
Alexa fluor 430 430 545
5-Carboxyfluorescein (5-FAM) 492 518
Alexa fluor 532 530 555
HEX 535 556
5-TAMRA 542 568
Cy3 550 570
TRITC 547 572
Alexa fluor 546 556 573
Alexa fluor 555 556 573
Dansyl 340 578
R-phycoerythrin (PE) (489) 565
Rhodamine Red-X 560 580
Tamara 565 580
Cy3 (512) 550
Cy3.5 581 596
Rox 575 602
Alexa fluor 568 578 603
Texas Red 589 615
Alexa fluor 594 590 617
Alexa fluor 621 639
Alexa fluor 633 650 668
Cy5 (625) 650
Alexa fluor 660 663 690
Cy5.5 675 694
TruRed 490; 675 695
Alexa fluor 680 679 702
Cy7 743 767