Other Florescent Dyes & Quenchers – VectorLabs

DBCO-dPEG®₁₂-carboxyfluorescein

Vector Laboratories R&D — Sat, 24 Feb 2024 02:18:07 +0000

Description
Specifications
Documents
References

Description

DBCO-dPEG®12-carboxyfluorescein, product number QBD-11812, permits fluorescein labeling of peptides, proteins, and other molecules using strain-promoted azide-alkyne cycloaddition (SPAAC). This compound combines the xanthene dye, 5(6)-carboxyfluorescein, with the popular click chemistry alkyne dibenzylcyclooctyne (DBCO) through a medium-length (40 atoms, 47.6 Å), single molecular weight, discrete PEG (dPEG®) spacer. The carboxyfluorescein label has an excitation wavelength (λex) of 498 nanometers (nm), and an emission wavelength (λem) of 528 nm. The molar absorptivity (ε) is 7.96×104 M-1 cm-1 at pH 8.0 and 498 nm.

Fluorescein and its derivatives are among the most popular dyes in use today for labeling proteins and cells. Unfortunately, these dyes are hydrophobic, and care must be taken to avoid over-labeling because over-labeling can result in quenching and possibly aggregation and precipitation of the conjugates through non-specific hydrophobic interactions.

DBCO is an increasingly popular choice for SPAAC chemistry, also known as “”copper-free click chemistry”” because it avoids the use of cytotoxic copper(I) ions and allows reactions to occur in and with living cells. Although DBCO may react with free sulfhydryl groups under some conditions, it is highly selective for azides. Because azides must be introduced artificially into proteins, DBCO is considered a bioorthogonal click chemistry reagent.

The introduction of a flexible dPEG® spacer between carboxyfluorescein and DBCO increases the molecule’s hydrodynamic volume and imparts water solubility to DBCO-dPEG®12-carboxyfluorescein. Thus, DBCO-dPEG®12-carboxyfluorescein provides a highly selective, flexible, water-soluble way to label proteins, peptides, and cells with carboxyfluorescein using a bio-orthogonal reagent designed to simplify analysis and characterization of the conjugate.

Specifications

Unit Size	1 mg, 5 mg
Molecular Weight	1234.34; single compound
Chemical formula	C₆₆H₇₉N₃O₂₀
CAS	N/A
Purity	> 97%
Spacers	dPEG® Spacer is 40 atoms and 47.6 Å
Shipping	Ambient
Typical solubility properties (for additional information contact Customer Support)	Methylene Chloride, Methanol, DMAC, or DMSO.
Storage and handling	-20°C; Always let come to room temperature before opening; be careful to limit exposure to moisture and restore under an inert atmosphere; stock solutions can be prepared with dry solvent and kept for several days (freeze when not in use). dPEG® pegylation compounds are generally hygroscopic and should be treated as such. This will be less noticeable with liquids, but the solids will become tacky and difficult to manipulate, if care is not taken to minimize air exposure.

Documents

References

Greg T. Hermanson, Bioconjugate Techniques, 2nd Edition, Elsevier Inc., Burlington, MA 01803, April, 2008 (ISBN-13: 978-0-12-370501-3; ISBN-10: 0-12-370501-0). Specifically see pp. 726-729 in his Chapter 18 on discrete PEG compounds for pegylation applications.

Greg T. Hermanson, Bioconjugate Techniques, 3rd Edition, Elsevier, Waltham, MA 02451, 2013, ISBN 978-0-12-382239-0; See chapter 18, Discrete PEG Reagents, pp.787-821, for a full overview of the dPEG® products.

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AMCA Acid

Vector Laboratories R&D — Tue, 19 Sep 2023 23:14:26 +0000

Description
Specifications
Abs/Em Spectra
Documents

Description

AMCA Acid (7-amino-4-methylcoumarin-3-acetic acid) is one of the most popular blue fluorescent tagging molecules. Often used as contrasting probes for double- and triple-labeling inimmunofluorescence microscopy, arrays and in situ hybridization. The desirable properties of AMCA dyes include a relatively large Stoke’s shift and resistance to photobleaching.

AMCA Acid is a reagent of choice for the preparation of custom activated esters that often are not commercially available. Examples of such activated esters include sulfo-NHS, TFP (2,3,5,6-Tetrafluorophenol), STP (4-Sulfo-2,3,5,6-Tetrafluorophenol, Sodium Salt). Another common application for non-activated carboxylic acid is peptide modification during solid phase synthesis, which usually requires in-situ activation with peptide coupling regents, for example HATU. AMCA Acid is also often used for control experiments, and for calibration.

Specifications

Unit Size	25 mg, 100 mg, 1000 mg
Reactivity	Primary amines (needs activation)
Abs/Em Maxima	345/450 nm
Extinction coefficient	19,000 cm-1M-1
Solubility	DMSO, DMF
Spectrally similar dyes	Alexa Fluor® 350, AMCA, DyLight® 350
Molecular weight	233.27
Storage Conditions	-20°C.
Shipping Conditions	Ambient temperature

Abs/Em Spectra

Documents

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AMCA NHS Ester

Vector Laboratories R&D — Tue, 19 Sep 2023 23:14:02 +0000

Description
Specifications
Abs/Em Spectra
Documents

Description

AMCA NHS Ester (succinimydyl-7-amino-4-methylcoumarin-3-acetic acid) is one of the most popular blue fluorescent tagging molecules. It is widely used to label antibodies, proteins and small drug molecules. Often used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization. The desirable properties of AMCA dyes include a relatively large Stoke’s shift and resistance to photobleaching.

AMCA NHS Ester reacts specifically and efficiently with a primary amine (e.g., side chain of lysine residues or aminosilane-coated surfaces) at pH 7-9 to form a stable, covalent amide bond. The NHS ester (or succinimidyl ester) is the most popular tool for conjugating dyes to the primary amines of protein or antibody (Lys), amine-modified oligonucleotides, and other amine-containing molecules.

Specifications

Unit Size	5 mg, 25 mg, 100 mg
Reactivity	Primary amines
Abs/Em Maxima	345/450 nm
Extinction coefficient	19,000 cm-1M-1
Solubility	DMSO, DMF
Spectrally similar dyes	Alexa Fluor® 350, AMCA, DyLight® 350
Molecular weight	330.30
Storage Conditions	-20°C.
Shipping Conditions	Ambient temperature

Abs/Em Spectra

Documents

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6,8-Difluoro-7-hydroxy-4-methylcoumarin NHS Ester

Vector Laboratories R&D — Tue, 19 Sep 2023 23:14:01 +0000

Description
Specifications
Abs/Em Spectra
Documents

Description

6,8-Difluoro-7-hydroxy-4-methylcoumarin NHS Ester (Marina Blue® NHS Ester) exhibit bright blue fluorescence emission near 460 nm is optimally excited by the intense 365 nm spectra line of the mercury-arc lamp and detect optimally with DAPI optical filter sets. Because the pKa value of 6,8-Difluoro-7-hydroxy-4-methylcoumarin derivatives are 2-3 log units lower compared to those of the corresponding 7-hydroxycoumarin conjugates, 6,8-Difluoro-7-hydroxy-4-methylcoumarin conjugates are strongly fluorescent even at neutral pH.

6,8-Difluoro-7-hydroxy-4-methylcoumarin NHS Ester reacts specifically and efficiently with a primary amine (e.g., side chain of lysine residues or aminosilane-coated surfaces) at pH 7-9 to form a stable, covalent amide bond. The NHS ester (or succinimidyl ester) is the most popular tool for conjugating dyes to the primary amines of protein or antibody (Lys), amine-modified oligonucleotides, and other amine-containing molecules.

Specifications

Unit Size	5 mg, 25 mg, 100 mg
Reactivity	Primary amines
Abs/Em Maxima	365/460 nm
Extinction coefficient	19,000 cm-1M-1
Solubility	DMSO, DMF
Spectrally similar dyes	Alexa Fluor® 350, AMCA, DyLight® 350
Molecular weight	367.26
Storage Conditions	-20°C.
Shipping Conditions	Ambient temperature

Abs/Em Spectra

Documents

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Difluorocarboxyfluorescein Azide, 6-isomer

Vector Laboratories R&D — Tue, 19 Sep 2023 23:13:36 +0000

Description
Specifications
Abs/Em Spectra
Protein Labeling Calculator
Documents

Description

2′, 7′-Difluorocarboxyfluorescein Azide, 6-isomer (also under Oregon Green 488 Azide (Oregon Green™ 6-Carboxamido-(6-Azidohexanyl), Triethylammonium Salt), 6-isomer name) is a bright, green-fluorescent azide-activated probe that reacts with terminal alkynes via a copper-catalyzed click reaction (CuAAC). It also reacts with strained cyclooctyne via a copper-free click chemistry reaction to form a stable triazole and does not require Cu-catalyst or elevated temperatures.

2′,7′-Difluorocarboxyfluorescein fluorinated analog of fluorescein that overcomes some of the key limitations of fluorescein, including greater photostability and a lower pKa (pKa ~ 4.7 versus 6.4 for fluorescein), making its fluorescence essentially pH insensitive in the physiological pH range.

Specifications

Unit Size	1 mg, 5 mg, 25 mg, 100 mg
Reactivity	Alkynes, cyclooctynes
Abs/Em Maxima	496/524 nm
Extinction coefficient	78,000 cm-1M-1
Solubility	DMSO, DMF
Spectrally similar dyes	Alexa Fluor® 488, DyLight® 488, Fluorescein, Oregon Green 488
Molecular weight	637.68
Storage Conditions	-20°C.
Shipping Conditions	Ambient temperature

Abs/Em Spectra

Protein Labeling Calculator

Protein name

Protein molecular weight (daltons)

Protein concentration (mg/mL)

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Enter only one — either volume or amount of protein to be labeled

Amount of protein to be labeled (mg)

Molecular weight of labeling reagent (Da)

Amount of labeling reagent used (mg)

Maximum concentration of DMSO (%) Leave blank or 0 if not used

Enter only one — either maximum concentration of DMSO or volume DMSO added to label

Volume of anhydrous DMSO added (µL)

Molar equivalents of labeling reagent used

Volume of DMSO required to make a stock solution (µL)

Volume of protein to be labeled (µL)

Amount of stock labeling reagent to be added (µL)

Amount of DMSO in labeling reaction (%)

Documents

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Difluorocarboxyfluorescein Cadaverine, 5-isomer

Vector Laboratories R&D — Tue, 19 Sep 2023 22:56:21 +0000

Description
Specifications
Abs/Em Spectra
Documents

Description

Difluorocarboxyfluorescein Cadaverine, 5-isomer (sold under Oregon Green™ 488 Cadaverine, 5-isomer name) is a carbonyl reactive building block used to modify carboxylic groups in the presence of activators (e.g. EDC, or DCC) or activated esters (e.g. NHS esters) through a stable amide bond. It also can be employed as a polar tracer and as a reactive dye for labeling proteins via a carboxylic acid moiety.

Difluorocarboxyfluorescein Cadaverineis a fluorinated analog of fluorescein that overcomes some of the key limitations of fluorescein, including greater photostability and a lower pKa (pKa ~ 4.7 versus 6.4 for fluorescein), making its fluorescence essentially pH insensitive in the physiological pH range.

Difluorocarboxyfluorescein Cadaverine, 5-isomer structurally is identical to Invitrogen’s Oregon Green™ 488 Cadaverine, 5-isomer

Specifications

Unit Size	5 mg, 25 mg, 100 mg
Reactivity	Aldehyde, carboxylic acid, ketone
Abs/Em Maxima	494/517 nm
Extinction coefficient	73,000 cm-1M-1
Solubility	DMSO, DMF, MeOH
Spectrally similar dyes	Alexa Fluor® 488, DyLight® 488, Fluorescein, Oregon Green 488
Molecular weight	496.46
Storage Conditions	-20°C.
Shipping Conditions	Ambient temperature

Abs/Em Spectra

Documents

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5-ROX (5-Carboxy-X-Rhodamine)

Vector Laboratories R&D — Tue, 19 Sep 2023 22:50:01 +0000

Description
Specifications
Abs/Em Spectra
Protein Labeling Calculator
Documents

Description

The carboxylic acid of 5-ROX is used for oligonucleotide labeling and automated DNA sequencing applications. Often a dye of choice for fluorescence resonance energy transfer (FRET) and fluorescence quenching applications. Conjugates of this dye have longer-wavelength spectra than the spectra of Lisaamine™ rhodamine B conjugates, but somewhat shorter-wavelength spectra than those of Texas Red™ conjugates.

Specifications

Unit Size	25 mg, 100 mg, 1000 mg
Reactivity	Primary amines
Abs/Em Maxima	570/591 nm
Extinction coefficient	93,000 cm-1M-1
Solubility	DMSO, DMF, MeOH
Spectrally similar dyes	Alexa Fluor® 568, TAMRA, CF™ 568
CAS	216699-35-3
Molecular weight	534.61
Storage Conditions	-20°C.
Shipping Conditions	Ambient temperature

Abs/Em Spectra

Protein Labeling Calculator

Protein name

Protein molecular weight (daltons)

Protein concentration (mg/mL)

Volume of protein to be labeled (µL)

Enter only one — either volume or amount of protein to be labeled

Amount of protein to be labeled (mg)

Molecular weight of labeling reagent (Da)

Amount of labeling reagent used (mg)

Maximum concentration of DMSO (%) Leave blank or 0 if not used

Enter only one — either maximum concentration of DMSO or volume DMSO added to label

Volume of anhydrous DMSO added (µL)

Molar equivalents of labeling reagent used

Volume of DMSO required to make a stock solution (µL)

Volume of protein to be labeled (µL)

Amount of stock labeling reagent to be added (µL)

Amount of DMSO in labeling reaction (%)

Documents

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5-ROX NHS Ester

Vector Laboratories R&D — Tue, 19 Sep 2023 22:49:59 +0000

Description
Specifications
Abs/Em Spectra
Protein Labeling Calculator
Documents

Description

5-Carboxy-X-rhodamine N-succinimidyl ester (5-ROX NHS Ester) is used as an amine coupling reagent to form 5-carboxy-X-rhodamine (ROX) derivatized compounds such as proteins, nucleic acids and drugs that may be analyzed by fluorescence resonance energy transfer (FRET) and fluorescence quenching applications. Labeling reagent for preparation of charge-modified dye-labeled ddNTPs to “direct-load” DNA sequencing. Conjugates of this dye have longer-wavelength spectra than the spectra of Lisaamine™ rhodamine B conjugates, but somewhat shorter-wavelength spectra than those of Texas Red™ conjugates.

Specifications

Unit Size	25 mg, 100 mg, 1000 mg
Reactivity	Primary amines
Abs/Em Maxima	582/606 nm
Extinction coefficient	93,000 cm-1M-1
Solubility	DMSO, DMF, MeOH
Spectrally similar dyes	Alexa Fluor® 568, TAMRA, CF™ 568
CAS	209734-74-7
Molecular weight	631.69
Storage Conditions	-20°C.
Shipping Conditions	Ambient temperature

Abs/Em Spectra

Protein Labeling Calculator

Protein name

Protein molecular weight (daltons)

Protein concentration (mg/mL)

Volume of protein to be labeled (µL)

Enter only one — either volume or amount of protein to be labeled

Amount of protein to be labeled (mg)

Molecular weight of labeling reagent (Da)

Amount of labeling reagent used (mg)

Maximum concentration of DMSO (%) Leave blank or 0 if not used

Enter only one — either maximum concentration of DMSO or volume DMSO added to label

Volume of anhydrous DMSO added (µL)

Molar equivalents of labeling reagent used

Volume of DMSO required to make a stock solution (µL)

Volume of protein to be labeled (µL)

Amount of stock labeling reagent to be added (µL)

Amount of DMSO in labeling reaction (%)

Documents

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5(6)-Carboxyrhodamine 110 NHS Ester

Vector Laboratories R&D — Tue, 19 Sep 2023 22:49:01 +0000

Description
Specifications
Abs/Em Spectra
Protein Labeling Calculator
Documents

Description

5(6)-Carboxyrhodamine 110 NHS Ester (also known as Rhodamine Green™ Carboxylic Acid, Succinimidyl Ester, Hydrochloride or 5(6)-CR 110, SE) is the nonsulfonated analog of the Alexa Fluor® 488 dye. The amine-reactive 5(6)-Carboxyrhodamine 110 NHS Ester can be used to create bright and photostable green-fluorescent bioconjugates with excitation/emission maxima ~502/527 nm.

The conjugates of this dye often used for Fluorescence Correlation Spectroscopy (FCS). For many applications, 5(6)-Carboxyrhodamine 110 NHS Ester is preferred over 5-(6)-carboxyfluorescein NHS ester or FITC because of its exceptional photostability and fluorescence insensitivity to pH (4-9).

Specifications

Unit Size	5 mg, 25 mg, 100 mg
Reactivity	Primary amine
Abs/Em Maxima	502/527 nm
Extinction coefficient	76,000 cm-1M-1
Solubility	DMSO, DMF
Spectrally similar dyes	Alexa Fluor® 488, DyLight® 488, Fluorescein, Oregon Green 488
Molecular weight	471.43
Storage Conditions	-50°C to -85°C
Shipping Conditions	Dry ice

Abs/Em Spectra

Protein Labeling Calculator

Protein name

Protein molecular weight (daltons)

Protein concentration (mg/mL)

Volume of protein to be labeled (µL)

Enter only one — either volume or amount of protein to be labeled

Amount of protein to be labeled (mg)

Molecular weight of labeling reagent (Da)

Amount of labeling reagent used (mg)

Maximum concentration of DMSO (%) Leave blank or 0 if not used

Enter only one — either maximum concentration of DMSO or volume DMSO added to label

Volume of anhydrous DMSO added (µL)

Molar equivalents of labeling reagent used

Volume of DMSO required to make a stock solution (µL)

Volume of protein to be labeled (µL)

Amount of stock labeling reagent to be added (µL)

Amount of DMSO in labeling reaction (%)

Documents

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5-Carboxyrhodamine 110 NHS Ester

Vector Laboratories R&D — Tue, 19 Sep 2023 22:48:35 +0000

Description
Specifications
Abs/Em Spectra
Protein Labeling Calculator
Documents

Description

5-Carboxyrhodamine 110 NHS Ester (also known as Rhodamine Green™ Carboxylic Acid, Succinimidyl Ester, Hydrochloride or 5-CR 110, SE) is the nonsulfonated analog of the Alexa Fluor® 488 dye. The amine-reactive 5(6)-Carboxyrhodamine 110 NHS Ester can be used to create bright and photostable green-fluorescent bioconjugates with excitation/emission maxima ~502/527 nm. For many applications, the dye is preferred over 5-(6)-carboxyfluorescein NHS ester or FITC because of its exceptional photostability and fluorescence insensitivity to pH (4-9).

Although the mixed isomers of Carboxyrhodamine 110 NHS Ester preferred, routinely used fluorescent dye for labeling proteins, peptides and nucleotides, purification of peptide and nucleotides labeled with 5(6) isomers might be troublesome due to significant signal broadening in HPLC purification. Peptides and nucleotides labeled with a single isomer usually give better resolution in HPLC purification that is often required in the conjugation processes.

Specifications

Unit Size	5 mg, 25 mg, 100 mg
Reactivity	Primary amine
Abs/Em Maxima	502/527 nm
Extinction coefficient	76,000 cm-1M-1
Solubility	DMSO, DMF
Spectrally similar dyes	Alexa Fluor® 488, DyLight® 488, Fluorescein, Oregon Green 488
Molecular weight	471.43
Storage Conditions	-50°C to -85°C
Shipping Conditions	Dry ice

Abs/Em Spectra

Protein Labeling Calculator

Protein name

Protein molecular weight (daltons)

Protein concentration (mg/mL)

Volume of protein to be labeled (µL)

Enter only one — either volume or amount of protein to be labeled

Amount of protein to be labeled (mg)

Molecular weight of labeling reagent (Da)

Amount of labeling reagent used (mg)

Maximum concentration of DMSO (%) Leave blank or 0 if not used

Enter only one — either maximum concentration of DMSO or volume DMSO added to label

Volume of anhydrous DMSO added (µL)

Molar equivalents of labeling reagent used

Volume of DMSO required to make a stock solution (µL)

Volume of protein to be labeled (µL)

Amount of stock labeling reagent to be added (µL)

Amount of DMSO in labeling reaction (%)

Documents

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