Dicarboxymethylene Blue NHS (DCMB)
Dicarboxymethylene Blue is a synthetic derivative of the methylene blue dye family that has been engineered to provide reactive carboxyl groups for biomolecule conjugation while maintaining favorable photophysical properties. Depending on the specific derivative, the dye exhibits fluorescence in the far-red to near-infrared (NIR) spectral region, where biological samples display lower autofluorescence and greater optical penetration than in the visible spectrum.
When conjugated to DNA or RNA oligonucleotides, Dicarboxymethylene Blue serves as a sensitive fluorescent reporter for molecular detection, hybridization assays, biosensor development, and fluorescence imaging. The carboxyl groups facilitate coupling through amino-modified oligonucleotides using standard amide-bond chemistry, allowing stable attachment to a wide variety of nucleic acid constructs.
Compared with shorter wavelength fluorophores, near-infrared dyes generally offer improved signal-to-background ratios in biological samples because tissue autofluorescence is significantly reduced at longer wavelengths. These properties make Dicarboxymethylene Blue particularly attractive for fluorescence imaging, multiplex detection, diagnostic assays, and advanced optical biosensors.
Bio-Synthesis offers custom Dicarboxymethylene Blue-modified oligonucleotides for DNA, RNA, PNA, LNA, siRNA, antisense oligonucleotides (ASOs), aptamers, PCR probes, hybridization probes, molecular beacons, and other custom nucleic acid constructs. The dye may be incorporated at the 5′ terminus, 3′ terminus, or attached through suitable internal amino linkers. It is also compatible with numerous additional modifications including quenchers, biotin, thiol modifiers, PEG linkers, click chemistry handles, GalNAc, cholesterol, peptide conjugates, lipid conjugates, and nanoparticle conjugates.
Typical research applications include:
- Near-infrared fluorescence imaging
- Hybridization probes
- Molecular beacon probes
- qPCR and fluorescence assays
- Biosensor development
- Aptamer imaging
- Optical diagnostics
- Multiplex fluorescence detection
- Photodynamic research
- Molecular interaction studies
Technical note
Dicarboxymethylene Blue NHS Ester" reagent (used for post-synthetic labeling of amino-modified oligonucleotides), oligonucleotide is first synthesized with a primary amine (e.g., Amino C6 or Amino-TEG), followed by conjugation with DCMB NHS ester. This distinguishes it from phosphoramidite-based modifications that are incorporated directly during automated synthesis.
Each modified oligonucleotide is synthesized using automated solid-phase phosphoramidite chemistry and is available with optional HPLC or PAGE purification. Comprehensive analytical characterization includes HPLC, LC-MS, MALDI-TOF, UV-Vis spectroscopy, and fluorescence quality control to verify sequence identity, purity, and successful dye incorporation.
| Property |
Typical Value |
| Modification |
Dicarboxymethylene Blue |
| Modification Class |
Near-Infrared Fluorescent Dye |
| Dye Family |
Methylene Blue Derivative |
| Spectral Region |
Far-red to Near-Infrared (derivative dependent) |
| Typical Attachment |
5′, 3′, or internal amino linker |
| Compatible Oligonucleotides |
DNA, RNA, PNA, LNA, siRNA, ASO, Aptamers |
| Primary Applications |
Fluorescence imaging, biosensors, hybridization assays, molecular diagnostics |
Research Use Only (RUO): Unless otherwise specified, Dicarboxymethylene Blue-modified oligonucleotides are supplied exclusively for research applications.
Product Information
Dicarboxymethylene Blue NHS (DCMB)
Electrochemical/redox label
-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at 20°C) in a nuclease-free environment should be stable for years.
References/Citations:
- Lubin AA, Plaxco KW. Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures. Accounts of Chemical Research. 2010;43(4):496-505.
- Xiao Y, Lubin AA, Heeger AJ, Plaxco KW. Label-free electronic detection of thrombin in blood serum by an aptamer-based sensor. Angewandte Chemie International Edition. 2005;44:5456-5459.
- Steel AB, Herne TM, Tarlov MJ. Electrochemical quantitation of DNA immobilized on gold. Analytical Chemistry. 1998;70:4670-4677.
- Hermanson GT. Bioconjugate Techniques. 3rd Edition. Academic Press; 2013.
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