Dye and fluorescent labelled compounds

Synthesis of dye and fluorescent labelled compounds.

Since our inception, we have received many requests for the synthesis of fluorescently labelled compounds. We are able to synthesise fluorescent compounds that are difficult to obtain commercially as well as those derived from commercially available fluorescent reagents. Listed below are some of the compounds we have synthesised (only compounds that are not subject to a confidentiality agreement for custom synthesis).

Click on a structural formula to view the list.


Rhodamine/Fluorescein	Cyanine	Bodipy

Dansyl	Pyranine	Coumarine

Acridine/Carbopyronin	Oxazine/Thioxazine	Phycocianine

Other fluorescent compounds

Performance requirements for fluorescent dyes.

Characteristic excitation and fluorescence wavelengths (Stokes shift), low pH dependence, high fluorescence intensity, high photostability and solubility (water solubility) are likely performance indicators.
The ability to excite dyes of multiple fluorescence wavelengths at one wavelength seems to allow for special applications.
Although we pride ourselves on being experts in the synthesis of specific structures, we do not have a good understanding of the relationship between the performance and structure of fluorescent dyes. We are now carefully investigating this point.

The rhodamine system is divided into fluorescein and rhodamine with the O replaced by N. The latter is said to be less PH dependent and more photostable. Alexa and HiLyte Fluor, which are improved versions of it, seem to have become more widely used in recent years.

Cyanine-based fluorescent dyes: characterised by high water solubility and inhibition of fluorescence decay by the addition of a sulphonic acid moiety.

BODIPY-based: is characterised by the stability of both absorption and emission wavelengths independent of pH and solvent type. It also has a larger Stokes shift than others and a sharp spectrum of signature.

Dye labelling and fluorescent labelling are frequently used as effective means of visualising proteins, antibodies, etc.
In most cases, this can be achieved by simply reacting the NHS-activated form of the dye compound with an amino group, but the number of requests for our services is increasing due to the difficulty of synthesis and purification, which requires specialised equipment and technology.

Problems with purity of dye-labelled compounds: sometimes stability problems or isomeric mixtures make it difficult to identify the products.
Multiple reaction points for the compound to be labelled or dye-labelled compounds, making it difficult to control the reaction.
Binding by methods other than amidation, such as Michael addition, click or esterification, will not work, even if the recipe is followed exactly.
Fluorescence-labelled compounds with structures that are not commercially available are required at short notice, but outsourcing would result in an extremely long lead time.
want to incorporate linkers and spacers into the dye labels to increase their water solubility.
want to replace the functional group with another.

There are a number of compounds in our synthesis results that cannot be disclosed due to confidentiality agreements.

Please do not hesitate to contact useven if your structure is not on the list.

We received several enquiries about bifunctional fluorescent substances, so we started development studies.

List of bifunctional (multifunctional) fluorescent compounds

Synthesis of fluorescently labelled compounds with PEG linkers.

Shinsei Chemical has been working for more than 15 years on the development of polyethylene glycol derivatives that are highly useful as hydrophilic linkers. We have synthesis technology for structures in which polyethylene glycol is used as an amphiphilic spacer and functional groups such as amino and carboxyl groups are inserted on the dye labels.

Direct amide bonding (A) is the simplest way to synthesise labelled compounds such as proteins, but the distance to the dye compound is too close and may affect the activity, so the insertion of an alkyl spacer or linker as in (B) is commonly used.
However, hydrophobic linkers cause aggregation in vivo, which not only prevents them from acting as spacers, but also causes non-specific adsorption.
The length of the PEG linker can range from about 3 repeating units to very long structures of 30 or more, depending on the purpose. Various types of linkers are available, including maleimide, click, ester and ether linkages as well as amide linkages at the end. The hydrophilicity is greatly improved by inserting or bonding PEG to fluorescent substances.

PEG linkers can be easily inserted from commercially available fluorescent dyes (terminal carboxylic acids, NHS active esters, isocyanates, isothiocyanates, etc.), showing a significant improvement in hydrophilicity.

Some of the synthesis results to date are presented below.

Shinsei Chemical has extensive experience in the synthesis of fluorescent dyes, and has the technology and experience in the synthesis of dyes directly bonded with PEG linkers without amide bonding or similar.

We have succeeded for the first time in synthesising a structure in which PEG is directly bonded to a Cyanine-based fluorescent dye.

This achievement has opened up the possibility of attaching PEGs of any length directly to cyanine-based fluorescent dyes without the need for amide bonding.

We are also investigating the binding of longer PEG chains and the synthesis of end structures other than carboxylic acids. Please feel free to contact us for more information, as we can accommodate your desired structure at a price range different from that of general contract synthesis.

Fluorescently labelled PEG list

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