New Fluorescent Labeling and Detection Products

For decades researchers have been using the famous Alexa Fluor® dyes developed by Molecular Probes for everything from flow cytometry to oligonucleotide labeling. These sulfonated forms of common fluorophores (coumarin, rhodamine, fluorescein, and cyanine) are thought to be more stable, brighter, and less pH-sensitive than the native molecules (Ref: Panchuk-Voloshina et al. 1999). Antibody users are likely most familiar with Alexa Fluor® 488 and Alexa Fluor® 594 which when used together allow for the simultaneous staining of one protein in green and another in red and can be used in combination with the blue nuclear dye DAPI.

Andy Fluor 488

The original Molecular Probes patents have likely limited the number of companies offering less expensive alternatives to the Alexa Fluor® dyes. Innovative dyes as DyLight® and IRDyes® have been developed and are used for specific applications, but direct alternatives for the standard Alexa Fluor® exitation and emission spectra dyes have been difficult/impossible to find…..until now.

Andy Fluor™ dyes are the next generation fluorescent dyes spanning the visible and near-infrared (IR) spectrum for labeling proteins and nucleic acids:

  • Andy Fluor™ 350
  • Andy Fluor™ 405
  • Andy Fluor™ 430
  • Andy Fluor™ 488
  • Andy Fluor™ 555
  • Andy Fluor™ 568
  • Andy Fluor™ 594
  • Andy Fluor™ 647
  • Andy Fluor™ 680
  • Andy Fluor™ 750

For oligonucleotide labeling by Nick translation, Random primer labeling, End-labeling with terminal deoxynucleotidyl transferase, Reverse transcription or PCR amplification Andy Fluor™ dNTPs are a nice low cost alternative to products such as ChromaTide® Alexa Fluor® 488-5-dUTP.

 

Label DNA RNA
Amine modification 5-Aminoallyl-dUTP 5-Aminoallyl-UTP
Biotin Biotin-11-dUTP Biotin-11-UTP
5-FAM 5-FAM-dUTP 5-FAM-UTP
5-FAM-X 5-FAM-X-dUTP 5-FAM-X-UTP
Andy Fluor 488 Andy Fluor™ 488-X-dUTP Andy Fluor™ 488-X-UTP
Andy Fluor 555 Andy Fluor™ 555-X-dUTP Andy Fluor™ 555-X-UTP
Andy Fluor 568 Andy Fluor™ 568-X-dUTP Andy Fluor™ 568-X-UTP
Andy Fluor 594 Andy Fluor™ 594-X-dUTP Andy Fluor™ 594-X-UTP
Andy Fluor 647 Andy Fluor™ 647-X-dUTP Andy Fluor™ 647-X-UTP
Cy3 Cy3-X-dUTP Cy3-X-UTP
Cy5 Cy5-X-dUTP Cy5-X-UTP

Originally developed by Applied BioProbes, the Andy Fluor™ dye labeled nucleotides are a small part of the rapidly growing fluorescence-based molecular biology offer from GeneCopoeia, Inc. Just as Alexa Fluor® has been the market leader for covalent fluorescent labeling of antibodies and oligonucleotides, SYBR® Green I, also produced by Molecular Probes, has historically been the leading dye for qPCR and “safe” agarose gel staining. GeneCopoeia has recently released their own: GreenView, GreenView Plus, and RedView agarose gel dyes.

 

Gel-stains

GreenView and RedView DNA Gel Stains very popular alternatives to Ethidium Bromide, as SYBR® Green-based Gel Stains have been demonstrated to offer a better safety profile by Ames test due to reduced DNA intercalation (Ref. Singer et al. 1998). Further optimization has resulted in dyes that also fail to cross the cell membrane of living cells resulting in an improved safety profile:

Cell permeability tests with Company A’s product, GreenView, GreenView Plus, and RedView. Hela cells were incubated at 37℃ with 1X Company A’s product, GreenView, GreenView Plus, and RedView for 30 min. GreenView Plus and RedView could not penetrate cell membranes to bind DNA in living cells, and were much safer than company A’s product, which rapidly entered cells and stained nuclei.

GreenView Plus and RedView fail to penetrate cell membranes to bind DNA in living cells.

 

Additional innovations from GeneCopoeia include the iQuant™ DNA Quantitation Kits to allow precise quantitation of DNA samples across a wide range of concentrations. Fluorescence-based DNA quantitation is highly sensitive and selective for DNA, relative to NanoDrop®-based absorbance readings (e.g. 260/280 ratios). Kits exist for double-stranded DNA or single-stranded DNA and can be adapted to microplate format using a fluorescence plate reader or tube format using fluorometers such as Qubit® or Quantus™:

 

iQuant

 

 

 

 Legal notes: Alexa Fluor®, SYBR®, Qubit® and ChromaTide® are registered trademarks of Life Technologies Corporation. DyLight® and NanoDrop® are registered trademarks of Thermo Fisher Scientific. IRDyes® is a registered trademark of Li-COR. Andy Fluor™ is a trademark of Applied Bioprobes. Quantus™ is a trademark of Promega.