Our fluorescence-labeled siRNA services support biotech companies, pharmaceutical research teams, academic laboratories, and assay development groups that need siRNA constructs for uptake visualization, transfection optimization, intracellular localization studies, and imaging-enabled RNAi workflows. Fluorescent siRNA is widely used when researchers need to confirm that a duplex actually enters cells, distinguish delivery failure from sequence failure, and correlate cellular uptake with downstream gene-silencing readouts.
We combine duplex design, fluorophore selection, label-position planning, custom synthesis, purification, analytical review, and application-focused support to help clients build siRNA constructs that are not only visible in imaging workflows, but also technically appropriate for functional RNAi studies. Whether you require a labeled experimental duplex, a scrambled uptake control, or a matched set of labeled and unlabeled sequences, our team can align the construct format with your imaging channel, cell model, and project objective.
Separating Delivery Failure from Sequence Failure: Many RNAi projects stall because weak knockdown can result either from poor siRNA design or from poor intracellular delivery. Fluorescence-labeled siRNA helps teams directly visualize uptake and distribution, making it easier to determine whether the next step should be sequence redesign, transfection optimization, or a different delivery strategy. For projects that move beyond simple lipofection screening, our RNA drug delivery system capabilities can support broader delivery-feasibility planning for research-stage studies.
Choosing a Label That Fits the Readout: A useful fluorescent siRNA must be matched to the instrument, filter set, assay background, and multiplexing plan. Teams often need guidance on whether a green-channel dye is enough for quick transfection checks, or whether an orange/red or far-red fluorophore is better for co-localization imaging, reduced autofluorescence, or multi-color workflows.
Preserving RNAi Function While Adding a Dye: Label placement matters. When gene silencing remains an important endpoint, direct labeling at the guide-strand 5' terminus is typically avoided because that region is closely tied to efficient RISC loading. In many standard duplex formats, labeling the passenger strand is the safer starting point for balancing visibility with retained RNAi performance.
Controlling Quality in a More Demanding Construct: Fluorescent siRNA is more than a standard duplex with a cosmetic add-on. Dye incorporation, linker choice, strand identity, duplex annealing behavior, and purification strategy can all affect background, handling, and assay reproducibility. We support build planning that accounts for both oligonucleotide chemistry and downstream imaging performance.
Building Better Controls for Imaging-Based RNAi: Researchers often need more than one construct to interpret results correctly, such as a labeled nonsilencing control, a matched unlabeled active duplex, or a labeled active siRNA paired with orthogonal knockdown confirmation. Our workflows can be coordinated with siRNA interference detection services so that uptake visualization and silencing verification are planned together instead of as separate outsourcing steps.
Our service platform is designed for teams that need more than basic synthesis. We support the full workflow from target review and duplex configuration through fluorophore placement, purification, control design, and application-oriented planning for microscopy, flow cytometry, high-content analysis, and transfection optimization.
By integrating RNA chemistry with assay-aware project support, we help reduce the risk of ordering a labeled duplex that looks acceptable on paper but performs poorly in the actual cell system, imaging setup, or RNAi workflow.
All our fluorescence-labeled siRNAs are purified by HPLC, and supplied in lyophilized powder. The quantity we can provide ranges from 2 OD to 250 OD.
| Catalog No. | Labelling | Quantity | Purification | Price |
| BRE-001 | 5' 6-FAM | 2 OD-250 OD | HPLC | Inquiry |
| BRE-002 | 3' 6-FAM | 2 OD-250 OD | HPLC | Inquiry |
| BRE-003 | 5' TET | 2 OD-250 OD | HPLC | Inquiry |
| BRE-004 | 3' TET | 2 OD-250 OD | HPLC | Inquiry |
| BRE-005 | 5' HEX | 2 OD-250 OD | HPLC | Inquiry |
| BRE-006 | 3' HEX | 2 OD-250 OD | HPLC | Inquiry |
| BRE-007 | 5' TAMRA | 2 OD-250 OD | HPLC | Inquiry |
| BRE-008 | 3' TAMRA | 2 OD-250 OD | HPLC | Inquiry |
| BRE-009 | 5' ROX | 2 OD-250 OD | HPLC | Inquiry |
| BRE-010 | 3' ROX | 2 OD-250 OD | HPLC | Inquiry |
| BRE-011 | 5' CY3 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-012 | 3' CY3 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-013 | 5' CY5 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-014 | 3' CY5 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-015 | 5' CY5.5 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-016 | 3' CY5.5 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-017 | 5' CY7 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-018 | 3' CY7 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-019 | 5' Dyomics681 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-020 | 3' Dyomics681 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-021 | 5' Dyomics781 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-022 | 3' Dyomics781 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-023 | 5' Texas Red | 2 OD-250 OD | HPLC | Inquiry |
| BRE-024 | 3' Texas Red | 2 OD-250 OD | HPLC | Inquiry |
| BRE-025 | 5' Methlyene Blue | 2 OD-250 OD | HPLC | Inquiry |
| BRE-026 | 3' Methlyene Blue | 2 OD-250 OD | HPLC | Inquiry |
| BRE-027 | 5' JOE | 2 OD-250 OD | HPLC | Inquiry |
| BRE-028 | 3' JOE | 2 OD-250 OD | HPLC | Inquiry |
| BRE-029 | 5' AMCA | 2 OD-250 OD | HPLC | Inquiry |
| BRE-030 | 3' AMCA | 2 OD-250 OD | HPLC | Inquiry |
| BRE-031 | 5' Dabcyl | 2 OD-250 OD | HPLC | Inquiry |
| BRE-032 | 3' Dabcyl | 2 OD-250 OD | HPLC | Inquiry |
| BRE-033 | 5' BHQ-1 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-034 | 3' BHQ-1 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-035 | 5' BHQ-2 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-036 | 3' BHQ-2 | 2 OD-250 OD | HPLC | Inquiry |
| BRE-037 | 5' other fluorescent dye | 2 OD-250 OD | HPLC | Inquiry |
| BRE-038 | 3' other fluorescent dye | 2 OD-250 OD | HPLC | Inquiry |
Fluorophore choice has a direct impact on signal clarity, imaging compatibility, and downstream assay interpretation. For fluorescence-labeled siRNA projects, the right dye is not only a matter of brightness, but also of instrument fit, spectral overlap, cellular background, and whether the construct will be used for simple uptake tracking or more complex multiplex imaging workflows.
| Fluorophore Type | Typical Detection Channel | Best For | Main Advantages | Main Considerations |
| FAM / Fluorescein-like | Green | Routine transfection checks, quick microscopy confirmation, simple uptake studies | Widely recognized, easy to use in standard fluorescence workflows, suitable for straightforward visualization | Higher background or autofluorescence may occur in some cell systems; not always ideal for complex multiplex imaging |
| HEX / VIC-like | Yellow-green | Alternative single-color assays, projects needing separation from common green markers | Useful when standard green-channel overlap should be reduced | Instrument compatibility should be checked before final dye selection |
| Cy3-like | Orange / Red | Confocal imaging, co-localization studies, higher-contrast cell imaging | Often provides stronger visual contrast than green dyes in cell-based imaging | Channel planning is still required when antibody stains or organelle dyes are used in parallel |
| TAMRA-like | Orange / Red | Imaging workflows that prefer classic orange-red detection | Familiar option for many fluorescence platforms and imaging assays | Signal behavior and filter compatibility should be reviewed for the specific instrument setup |
| Cy5-like | Far-red | Multiplex imaging, reduced-background studies, advanced localization work | Useful for experiments requiring better spectral separation and lower visible-range interference | Some imaging systems are less optimized for far-red detection, so equipment fit should be confirmed |
| Alexa Fluor-like far-red options | Far-red | High-content imaging, multi-color experimental panels, complex cell studies | Suitable for broader multiplex strategies and imaging panel design | Final choice depends on available filters, co-stains, and desired signal intensity |
| Custom fluorophore options | Variable | Specialized imaging systems, pre-defined assay panels, platform-specific workflows | Allows closer alignment with existing instrument channels or internal assay standards | Requires case-by-case review of synthesis feasibility, purification, and downstream application compatibility |
Label position is one of the most important design variables in fluorescence-labeled siRNA development. The strand selected for fluorophore attachment and the terminal position of that label can affect not only visualization performance, but also duplex behavior, guide-strand function, and how reliably fluorescence data can be interpreted alongside gene-silencing results.
| Labeling Position | Typical Use Case | Functional Impact Risk | Recommended When | Notes |
| Sense Strand 5' End | Uptake tracking, transfection monitoring, non-functional imaging controls | Low to moderate | A visible duplex is needed primarily for delivery or imaging rather than maximum silencing performance | Often a practical starting point for labeled control siRNA constructs |
| Sense Strand 3' End | Imaging plus a more conservative duplex architecture | Low | The project requires fluorescence labeling with limited interference to standard duplex behavior | Commonly considered for active or control constructs where balanced design is preferred |
| Antisense Strand 5' End | Special-purpose builds only | High | Used only when there is a strong project-specific reason and functional testing is planned | This position is generally approached with caution because guide-strand 5' functionality is important for efficient RNAi activity |
| Antisense Strand 3' End | Functional labeled siRNA with guide-strand involvement still under review | Moderate | A guide-strand-labeled construct is required for a defined experimental reason | More suitable for carefully planned research builds than routine transfection controls |
| Dual-Labeled Duplex | Imaging-focused assays, trafficking studies, high-visibility visualization | High | Signal intensity is prioritized over preservation of typical RNAi performance | Usually better suited to imaging or delivery studies than to knockdown-sensitive experiments |
| Labeled Control + Unlabeled Active Pair | Functional RNAi studies with uptake confirmation | Low overall experimental risk | The team wants to visualize delivery while preserving a separate unlabeled construct for clean activity comparison | Often one of the most informative formats for combined imaging and gene-silencing workflows |
A well-designed control strategy is often more important than the fluorescent siRNA itself. In many RNAi imaging experiments, fluorescence confirms that material is present, but does not by itself prove productive delivery or target-specific silencing. The table below outlines how different study goals typically map to different control sets and readout strategies.
| Experimental Goal | Recommended siRNA Set | Why It Matters | Typical Readout |
| Transfection efficiency check | Labeled nonsilencing control | Confirms whether cells receive the duplex without introducing target-specific silencing effects | Fluorescence microscopy, flow cytometry, positive-cell counting |
| Uptake comparison across delivery systems | Labeled control duplex plus optional labeled active duplex | Helps compare carrier performance while reducing confusion between uptake and knockdown outcomes | Cellular fluorescence intensity, uptake-positive population, imaging distribution |
| Functional gene knockdown with visualization | Labeled active siRNA plus matched unlabeled active siRNA | Allows direct comparison between visible uptake and true silencing performance | Imaging signal, mRNA reduction, protein knockdown |
| Localization or trafficking study | Labeled active or labeled control duplex paired with co-staining markers | Supports intracellular distribution analysis and organelle or compartment comparison | Confocal imaging, co-localization analysis, time-course microscopy |
| Assay development or platform setup | Labeled negative control, unlabeled active siRNA, and project-specific reference duplex | Produces a more interpretable baseline for imaging, RNAi activity, and workflow validation | Signal window analysis, transfection reproducibility, assay qualification data |
| Delivery troubleshooting in hard-to-transfect cells | Labeled control duplex, unlabeled active duplex, and optional positive transfection reference | Helps determine whether weak knockdown is caused by poor uptake, poor release, or poor sequence performance | Uptake visualization, viability check, knockdown correlation |
| High-content or multiplex imaging workflow | Channel-matched labeled control plus unlabeled or differently configured active duplex | Prevents fluorescence planning from distorting the interpretation of functional RNAi results | High-content image analysis, multi-parameter cell profiling |
| Comparative reagent or formulation screening | Shared labeled control across groups plus selected active constructs | Improves consistency when comparing multiple transfection reagents or formulation conditions | Population-level uptake, image-based ranking, workflow optimization |
Our workflow is structured for research teams that need a technically consistent path from design brief through labeled duplex delivery, rather than treating fluorophore incorporation as a disconnected modification request.
We review the target gene or control requirement, species, intended cell model, detection method, and whether the construct is meant for uptake tracking, localization, transfection optimization, or combined imaging and silencing studies.
The team evaluates duplex architecture, fluorophore family, label position, and the need for scrambled controls, unlabeled comparators, or additional modified variants so the final order supports interpretable results.
Once the build strategy is agreed, we define strand format, terminal functionality, purification expectations, and any special considerations related to imaging channel compatibility or functional RNAi preservation.
The required strands are synthesized, fluorophore incorporation is completed according to the approved design, and the final duplex is assembled under conditions appropriate for the intended research-use application.
Purity, construct identity, and final build consistency are reviewed before release so clients receive a labeled siRNA that is suitable for imaging workflows and not compromised by avoidable chemistry-related variability.
Final materials are delivered with project-specific technical information, and where needed we can help clients plan the next step, such as unlabeled activity comparison, control expansion, modified rebuilds, or additional RNAi support services.
Fluorescent siRNA projects often fail when they are treated as routine oligo orders instead of application-driven duplex engineering tasks. Our service model is built to bridge that gap by combining RNA chemistry knowledge with the practical realities of imaging-based RNAi experiments.
Fluorescence-labeled siRNA can support far more than basic transfection checks. When properly designed, these constructs become useful tools for delivery assessment, cell biology, assay troubleshooting, and mechanism-focused RNAi experiments.
Fluorescence-labeled siRNA enables real-time tracking of transfection efficiency, optimization of delivery conditions, intracellular distribution studies, and multi-labeling experiments using microscopy and flow cytometry.
We offer comprehensive dye options including FAM, Cy3, Cy5, Alexa Fluor series, and other fluorophores to match various detection systems and experimental requirements.
Our optimized labeling strategies maintain siRNA silencing activity while providing strong fluorescence signals, with validation data confirming minimal impact on gene knockdown efficiency.
Yes, we provide dual-labeling services with compatible dye combinations for advanced applications such as FRET studies and multi-channel detection experiments.
All fluorescence-labeled siRNAs undergo rigorous HPLC purification, mass spectrometry verification, and functional validation to guarantee optimal performance in both imaging and gene silencing applications.
We offer flexible synthesis scales from research quantities (2 OD) to bulk production (250 OD), with customization options for specialized labeling requirements.
Whether you need a fluorescent siRNA for rapid transfection monitoring, intracellular localization imaging, delivery-system screening, or a functionally relevant labeled duplex paired with orthogonal controls, our team can help define the right construct for the job. We support projects ranging from standard passenger-strand labeling through more advanced modified and multifunctional siRNA builds, with planning that takes sequence logic, fluorophore choice, purification needs, and downstream assay use into account. To accelerate project evaluation, please share the target gene or sequence, species, preferred fluorophore, desired labeling position, intended cell model, and whether you need active siRNA, negative controls, or matched unlabeled comparators. Contact us to discuss your fluorescence-labeled siRNA requirements.
