These modifications impart optical properties to oligonucleotides, enabling their use in highly sensitive detection and quantification. By covalently attaching fluorescent reporter groups (fluorophores) and corresponding quencher groups to oligonucleotides, various functional fluorescent probes can be constructed.
Key applications include but are not limited to: qPCR probes (e.g., TaqMan® probes, MGB probes), genotyping probes (e.g., SNP genotyping), STR detection probes, and molecular beacons.
Fluorophores
A fluorophore (or fluorochrome) is a fluorescent chemical compound that can absorb light at a specific wavelength (excitation) and subsequently re-emit light at a longer, lower-energy wavelength (emission). This process is called fluorescence.
| Sub-category | Name (full) | Abbreviation / Code | Product Type | Applies to | Position | Function & mechanism (including like products) | Typical applications |
| Cyanine dyes | Cyanine 3 | CY3 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Green fluorescent dye (λex 550 nm / λem 570 nm). Bright, photostable, and compatible with most fluorescence platforms. Commonly paired with CY5 as a FRET donor. | FISH, FRET-based detection, gel imaging, multiplex qPCR |
| Cyanine dyes | Cyanine 5 | CY5 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Far-red fluorescent dye (λex 650 nm / λem 670 nm). Excellent for low-autofluorescence imaging windows. FRET acceptor for CY3 donor pairs. | Single-molecule studies, FRET, multiplex NGS, bioimaging |
| Cyanine dyes | Cyanine 5.5 | CY5.5 | Like | DNA / RNA | 5′ / 3′ | Near-infrared dye (λex 675 nm / λem 695 nm). Extended far-red emission for tissue imaging with reduced background. Used in NIR in vivo imaging. | In vivo imaging, NIR detection, tissue-level diagnostics |
| Cyanine dyes | Cyanine 7 | CY7 | Like | DNA / RNA | 5′ / 3′ / Internal (dT) | Near-infrared dye (λex 750 nm / λem 773 nm). Minimal tissue autofluorescence at this wavelength. Suited for deep-tissue imaging. | Deep-tissue imaging, multiplexed NIR assays |
| Cyanine dyes | Cyanine 5 maleimide | CY5-M | Like | DNA / RNA | 5′ / Internal (dT, dC) | CY5 variant with maleimide reactive group for thiol conjugation. Used for site-specific labeling of thiol-containing oligonucleotides or proteins. | Protein-oligo conjugation, site-specific labeling |
| FAM / fluorescein family | Fluorescein (FAM) | FAM | Generic | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Standard green fluorescent dye (λex 494 nm / λem 520 nm). Most widely used reporter in qPCR TaqMan probes. pH-sensitive above 7; stable in standard assay buffers. | qPCR TaqMan reporter, gel electrophoresis, FRET studies |
| FAM / fluorescein family | FITC (Fluorescein isothiocyanate) | FITC | Like | DNA / RNA | 5′ / 3′ | Fluorescein derivative reactive toward amines. Commonly used for direct protein or antibody labeling; can be introduced via amino-modified oligos. | Antibody conjugation, cell-surface labeling, immunofluorescence |
| FAM / fluorescein family | HEX (Hexachlorofluorescein) | HEX | Generic | DNA / RNA | 5′ / 3′ | Yellow-green fluorophore (λex 535 nm / λem 556 nm). Spectrally shifted from FAM; used in multiplexed qPCR as a second channel reporter. | Multiplexed qPCR (2nd channel), SNP genotyping |
| FAM / fluorescein family | TET (Tetrachlorofluorescein) | TET | Generic | DNA / RNA | 5′ / 3′ | Yellow-green fluorophore similar to HEX (λex 521 nm / λem 536 nm). Older channel dye; still used in legacy diagnostic panels. | Legacy qPCR panels, fragment analysis |
| FAM / fluorescein family | JOE | JOE | Generic | DNA / RNA | 5′ / 3′ | Yellow fluorophore (λex 527 nm / λem 548 nm). Used as a second dye in multiplex PCR and Sanger sequencing. | Multiplex PCR, Sanger sequencing |
| FAM / fluorescein family | VIC | VIC | Like | DNA / RNA | 5′ / 3′ | Proprietary fluorophore used in TaqMan SNP genotyping assays (Life Technologies). Compatible with TaqMan allelic discrimination workflows. | SNP genotyping, allelic discrimination |
| Rhodamine / TAMRA family | TAMRA (Tetramethylrhodamine) | TAMRA / TAM | Like | DNA / RNA | 5′ / 3′ | Orange-red fluorophore (λex 555 nm / λem 580 nm). Used both as a reporter and as a non-fluorescent quencher in TaqMan-style probes when placed at 3′. | qPCR probes (reporter or quencher), gel imaging |
| Rhodamine / TAMRA family | ROX (Carboxy-X-rhodamine) | ROX | Like | DNA / RNA | 5′ / 3′ | Red fluorophore (λex 585 nm / λem 605 nm). Used as a passive reference dye in real-time PCR to normalize well-to-well fluorescence variation. | Real-time PCR reference dye, multiplexed detection |
| Rhodamine / TAMRA family | Texas Red (TXR) | TXR | Like | DNA / RNA | 5′ / 3′ | Far-red rhodamine dye (λex 596 nm / λem 620 nm). High photostability in fixed-cell imaging. Minimal spectral overlap with FITC and CY5. | Multicolor FISH, immunofluorescence, confocal microscopy |
| Rhodamine / TAMRA family | ET-TAMRA | ET-TAMRA | Like | DNA / RNA | 5′ / 3′ | Energy transfer TAMRA — brighter variant produced via intramolecular energy transfer. Provides stronger signal than standard TAMRA in probe assays. | qPCR, SNP genotyping, bright-probe applications |
| Rhodamine / TAMRA family | ET-ROX | ET-ROX | Like | DNA / RNA | 5′ / 3′ | Energy transfer ROX variant. Enhanced brightness for low-copy-number detection. | Sensitive qPCR, low-template diagnostics |
| Alexa Fluor series | Alexa Fluor 350 | AF350 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Blue-UV fluorophore (λex 349 nm / λem 442 nm). High photostability and brightness relative to DAPI or coumarin. Requires UV excitation. | Multicolor imaging (UV channel), microarray |
| Alexa Fluor series | Alexa Fluor 488 | AF488 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Bright green fluorophore (λex 495 nm / λem 519 nm). Spectrally similar to FAM but more photostable and pH-insensitive. Widely used in confocal microscopy. | Cell imaging, flow cytometry, FISH, single-molecule |
| Alexa Fluor series | Alexa Fluor 532 | AF532 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Yellow-green fluorophore (λex 532 nm / λem 554 nm). Excellent match for 532 nm laser excitation. Standard two-color microarray dye. | Two-color microarray (Cy3 channel substitute), imaging |
| Alexa Fluor series | Alexa Fluor 546 | AF546 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Orange-yellow fluorophore (λex 556 nm / λem 573 nm). Used in multicolor imaging where spectral separation from FAM/CY3 is needed. | Multicolor FISH, co-localization studies |
| Alexa Fluor series | Alexa Fluor 594 | AF594 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Red fluorophore (λex 590 nm / λem 617 nm). Excellent photostability for live-cell long-exposure imaging. | Live-cell imaging, FRET, co-localization |
| Alexa Fluor series | Alexa Fluor 647 | AF647 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Far-red fluorophore (λex 650 nm / λem 668 nm). Gold standard for super-resolution (STORM/PALM) due to high photon count and blinking behavior. | STORM/PALM super-resolution, flow cytometry, single-molecule |
| Alexa Fluor series | Alexa Fluor 680 / 700 / 750 | AF680 / AF700 / AF750 | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Near-infrared series (λem 702–780 nm). Used for in vivo and tissue imaging due to reduced autofluorescence in the NIR window. | In vivo imaging, tissue diagnostics, NIR multiplex |
| ATTO dyes | ATTO 425 / 550 / 565 / 594 / 655 / 700 / Rho11 | ATTO series | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | High-brightness, photostable fluorophores from the ATTO-TEC series. ATTO dyes cover the full visible and NIR spectrum with high quantum yields. Preferred for single-molecule and super-resolution applications. | Single-molecule FRET, STORM, confocal imaging, qPCR |
| Quasar dyes | Quasar 570 / 670 / 705 | Quasar series | Like | DNA / RNA | 5′ / 3′ / Internal (dT, dC) | Quasar dyes (Biosearch Technologies) are cyanine-based fluorophores with improved water solubility and photostability. Q570 approximates CY3, Q670 approximates CY5. | Molecular beacons, FISH, qPCR multiplex |
| Other fluorophores | NED / PET / RHO 101 / SF670 / YakYellow | NED / PET / others | Like | DNA | 5′ / 3′ | Specialty dyes used in genotyping, fragment analysis, and multiplex SNP panels. NED and PET are Applied Biosystems dyes for capillary electrophoresis. | Fragment analysis, STR typing, capillary electrophoresis |
| Other fluorophores | Methylene Blue | MB | Like | DNA / RNA | 5′ / 3′ | Electroactive and photosensitizing dye. Used in electrochemical biosensors for signal transduction at electrode surfaces. | Electrochemical DNA sensors, aptamer biosensors |
| Other fluorophores | Ferrocene | Fc | Like | DNA / RNA | 5′ / 3′ | Organometallic redox tag. Provides a well-defined electrochemical signal for electrochemical DNA detection without optical equipment. | Electrochemical biosensors, DNA diagnostics on electrode platforms |
Quenchers
A quencher is a molecule that, upon coming very close to a fluorophore, reduces or eliminates (quenches) its fluorescence. Quenchers work by absorbing the energy from the excited fluorophore and dissipating it as heat (via a mechanism called Förster Resonance Energy Transfer, or FRET) or by simply blocking the excitation light.
| Sub-category | Name (full) | Abbreviation / Code | Product Type | Applies to | Position | Function & mechanism (including like products) | Typical applications |
| Black Hole Quenchers (BHQ) | BHQ1 (Black Hole Quencher 1) | BHQ1 | Like | DNA / RNA | 5′ / 3′ | Non-fluorescent dark quencher absorbing 480–580 nm. Paired with FAM, HEX, TET, or TAMRA reporters. FRET-based quenching; generates no background fluorescence. | qPCR TaqMan probes, molecular beacons, hybridization probes |
| Black Hole Quenchers (BHQ) | BHQ2 (Black Hole Quencher 2) | BHQ2 | Like | DNA / RNA | 5′ / 3′ | Non-fluorescent dark quencher absorbing 559–670 nm. Ideal partner for CY3, TAMRA, ROX, CY5, and Quasar 570. | qPCR probes (CY3/ROX/CY5 channel), dual-labeled probes |
| Black Hole Quenchers (BHQ) | BHQ3 (Black Hole Quencher 3) | BHQ3 | Like | DNA / RNA | 3′ | Non-fluorescent dark quencher absorbing 620–730 nm. Designed for far-red and NIR reporters including CY5, CY7, Quasar 670, and Quasar 705. | Far-red qPCR probes, NIR multiplexing |
| MGB quenchers | MGB (Minor Groove Binder) | MGB | Like | DNA / RNA | 3′ | Binds in the minor groove of the DNA duplex, increasing probe Tm by ~15°C. Allows shorter probe design (13–18 nt) with high specificity. Most widely used in SNP discrimination assays. | TaqMan SNP genotyping, allelic discrimination, short-probe qPCR |
| MGB quenchers | MGB-PLUS | MGB-PLUS | Like | DNA | 3′ | Enhanced MGB derivative providing higher Tm elevation than standard MGB. Suitable for AT-rich targets where standard probes are difficult to design. | AT-rich target detection, difficult sequence qPCR |
| Other quenchers | DABCYL | DAB | Like | DNA / RNA | 5′ / 3′ / Internal (dT) | Classic azo dye quencher absorbing 400–500 nm. Earliest quencher used in molecular beacons. Lower quenching efficiency vs BHQ for red-shifted reporters. | Molecular beacons, FRET probes, historical reference assays |
| Other quenchers | Eclipse Dark Quencher | ECL | Like | DNA | 3′ | Broad-spectrum dark quencher (400–625 nm) optimized for 3′-end probe labeling. Reduces background signal in probe-based detection. | qPCR probes, hybridization probes |
| Other quenchers | BBQ-650 | BBQ-650 | Like | DNA | 3′ | Far-red dark quencher (absorbs 580–680 nm). Optimal partner for CY5 and Quasar 670 in far-red probes. | Far-red molecular beacons, CY5-labeled probe quenching |
| Other quenchers | BKHFQ (BHQ-based dual quencher) | BKHFQ | Like | DNA | 3′ | Proprietary combined quencher for dual-labeled long probes (>40 nt). Reduces internal fluorescence signal from incomplete quenching in long sequences. | Long probe designs (40+ nt), STR probes, hybridization |
| Other quenchers | QSY7 | QSY7 | Like | DNA | 3′ | Non-fluorescent dark quencher (λabs 560 nm). FRET-based; accepts energy from FAM, FITC, TAMRA. Used in protease activity assays. | Protease-activated oligonucleotide probes |
Modification: FAM, BHQ1
Download the order form "Tsingke_DNA_Order Form.1.1.1.250815.csv" for DNA modifications or "Tsingke_RNA_Order Form.1.1.1.250815.csv" for RNA modifications below and email it to info@tsingke.com.cn, or "Send Your Request" to submit your inquiry online. Please refer to "Tsingke_DNA_Modification List_1.1.1.250815.csv" or "Tsingke_RNA_Modification List_1.1.1.250815.csv" sheet to paste special base and internal modification codes in your sequence.
Commonly used fluorescent dyes include FAM, TET, HEX, TAMRA, ROX, Cy3, and Cy5. These dyes cover a broad range of excitation and emission wavelengths and are widely applied in PCR, hybridization assays, and fluorescence-based detection.
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