SYBR Green II (Ionic form) , CAS No.178919-00-1

CAS: 178919-00-1 Cat. No.: S1452176 Summenformel: C₂₈H₂₈N₃OS+ Molekulargewicht: 454.61

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Übersicht

SYBR Green II (Ionic form) is a fluorescent nucleic acid dye that mainly binds single-stranded nucleotides. SYBR Green II is sensitive to oligonucleotides or larger nucleic acid polymers in a variety of cells and gels. SYBR Green II can be used to study cell structure, membrane integrity or function, and cell cycle distribution. Wavelength 484/515 nm.

Specifications

Storage

Store at -20°C

Verschickt in

Ice chest + Ice pads

Dieses Produkt erfordert Kühlkettenversand. Grundversand und andere Economy-Optionen sind nicht verfügbar.

Namen und Kennungen

• Molekulargewicht: 454.61

Application Protocols

The following protocols are general literature/practice guidelines for SYBR Green II-type RNA stains and are not item-specific specifications. Optimize for your gel system and imaging hardware.

A. Post-staining RNA agarose gels (formaldehyde/MOPS)

• Run gel and complete electrophoresis. Rinse gel 2×10 min in nuclease-free water or 1× MOPS to reduce formaldehyde background.
• Prepare a working dye solution in 1× MOPS or nuclease-free water (keep protected from light).
• Incubate gel 15–40 min with gentle rocking in the dark. For thick gels or low-abundance RNA, extend time.
• Optional: Brief 5–10 min rinse in buffer/water to decrease background.
• Image using blue/green excitation and a 520–550 nm emission filter.

B. Post-staining RNA PAGE (TBE-urea)

• After electrophoresis, remove urea by a 5–10 min rinse in 1× TBE or nuclease-free water.
• Stain 10–30 min in dye working solution with gentle agitation in the dark; rinse briefly if needed.
• Image as above.

C. Solution-based RNA quantification (microplate)

• Prepare standards (e.g., ribosomal RNA) and samples in nuclease-free buffer (TE or similar).
• Add dye to each well to a constant final concentration; incubate a few minutes until signal stabilizes.
• Read fluorescence with appropriate excitation/emission settings; generate a standard curve for quantification.

General tips: Use RNase-free consumables, minimize light exposure, and prepare single-use aliquots to maintain consistency.

Biological Roles

This product is a synthetic fluorescent dye used as a research tool; it has no intrinsic biological role in living systems. The following describes its function in biochemical assays (literature/general):

• Nucleic acid binding: Exhibits strong, noncovalent binding to nucleic acids, with enhanced affinity and fluorescence for RNA and single-stranded nucleic acids relative to double-stranded DNA.
• Fluorescence turn-on: The dye’s quantum yield increases dramatically upon binding due to restricted intramolecular rotations and reduced nonradiative decay in the nucleic-acid environment.
• Assay compatibility: Suitable for visualizing RNA integrity (rRNA bands), small RNAs (tRNA, miRNA precursors in PAGE), and single-stranded oligos. It can support solution-based quantification workflows where fluorescence is proportional to nucleic acid mass over a defined dynamic range.
• Buffer effects: Ionic strength, pH, and denaturants modulate binding and signal; optimized buffers (e.g., TBE-urea for PAGE, MOPS for agarose/formaldehyde gels) are preferred for consistent results.

No medical or clinical claims are made. Use is restricted to research applications such as electrophoresis, blotting pre-checks, and fluorescence-based quantification in vitro.

Buffer Applications

As a nucleic-acid stain, SYBR Green II is typically employed in electrophoresis and solution assay buffers. Item-specific buffer instructions are not provided; the following reflects common laboratory practice for this dye class.

• Electrophoresis (RNA):

  • Denaturing agarose RNA gels: MOPS/formaldehyde running buffer and gel matrix. After electrophoresis, rinse gels in nuclease-free water or 1× MOPS to remove formaldehyde, then post-stain with dye in buffer.
  • Denaturing PAGE (urea-PAGE): TBE-urea systems are common. Post-stain in 1× TBE or nuclease-free water to visualize small RNAs/oligos.

• Post-stain approach (general):

  • Prepare a working dye solution in 1× buffer (TBE or MOPS) or nuclease-free water; incubate gel with gentle agitation (typical 10–40 min), protected from light. Brief destaining in buffer/water can lower background.

• Solution assays:

  • Fluorescence measured in TE or nuclease-free water with appropriate ionic strength; calibrate using RNA standards.

• Practical tips:

  • Use RNase-free consumables and buffers. Filter buffers when feasible.
  • Optimize dye concentration and staining time for gel thickness and target mass; excessive dye may increase background or quench signal.
  • Imaging: Use blue/green excitation with a 520–550 nm emission capture range where possible.

Green Alternatives

SYBR Green II (ionic form) is commonly used as a safer and more sensitive alternative to traditional intercalating dyes like ethidium bromide (EtBr) for RNA/single-stranded nucleic acid detection.

Context and comparison (literature/general; not item-specific specifications):

• Ethidium bromide vs SYBR Green II:

  • Hazard profile: EtBr is mutagenic with challenging waste handling. SYBR dyes are often marketed as lower-hazard, though they should still be handled as potentially hazardous intercalators with appropriate PPE and waste controls.
  • Sensitivity: SYBR Green II typically provides higher sensitivity for RNA and ssDNA than EtBr, enabling lower mass detection.
  • Imaging: Optimized for blue-light excitation, allowing use of less damaging illumination compared to UV required for EtBr.

• SYBR Safe/SYBR Gold vs SYBR Green II:

  • SYBR Safe is formulated for reduced hazard and blue-light excitation; SYBR Gold offers very high sensitivity across nucleic acids. Choice depends on target (RNA vs DNA) and instrument filters.

Sustainability practices (general):

• Replace UV transillumination with blue/green LED sources to reduce energy use and sample damage.
• Use minimal effective dye concentration and adopt post-staining (rather than gel pre-staining) to reduce total dye usage and waste.
• Segregate dye-containing waste for appropriate disposal; consider in-gel destaining and reuse of staining solutions when validated to maintain sensitivity.

Pharmaceutical Uses

Not applicable. SYBR Green II is a laboratory fluorescent stain for nucleic acids and is not used as a pharmaceutical active ingredient or excipient in drug products. No pharmacopeial monograph or formulation role is specified for this item.

For manufacturing environments that utilize nucleic-acid stains for in-process analytics, handle exclusively as a research-use-only reagent and segregate from GMP drug product streams. Consult your quality unit and regulatory guidance before any use in controlled environments.

Physical Properties

Item-specific specifications are not provided for this catalog entry; consult the CoA/SDS for authoritative values.

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular Weight: Not specified for this item; refer to CoA/Spec Sheet.
• Solubility (item-specific): Not specified for this item; refer to CoA/Spec Sheet.
• Melting/boiling points, density, refractive index: Not specified for this item; refer to CoA/Spec Sheet.

Photophysical characteristics (literature/general for SYBR Green II in nucleic-acid complexes; not item specifications):

• Excitation/Emission: Typically excites in the blue-green (~480–500 nm) and emits green (~530–540 nm) when bound to RNA; exact maxima depend on buffer, ionic strength, and binding environment.
• Quantum yield: Strongly enhanced upon binding to nucleic acids and very low when free in solution (environment-sensitive turn-on behavior).
• Binding preference: Reported to preferentially stain RNA/single-stranded nucleic acids with reduced background from double-stranded DNA compared to SYBR Green I.
• Recommended solvent for stock solutions (general practice): Anhydrous DMSO or water, protected from light; final working solutions are typically prepared in electrophoresis buffers (e.g., TBE/TBE-urea, MOPS) or nuclease-free water.

Practical notes (general):

• Photosensitive: minimize light exposure during handling and staining to preserve signal.
• Fluorescence is significantly increased upon binding to target; background signal can be managed by brief rinses or buffer exchanges after staining.

Quality and Grades

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.

Context for this product type (general):

• Fluorescent nucleic-acid stains are commonly supplied at high purity to minimize background fluorescence and nuclease contamination. Some vendors provide “molecular biology grade” to indicate testing for DNase/RNase; however, this designation is not specified for this item.
• Ionic (salt) form: Many cyanine dyes are supplied as salts to enhance stability and solubility. The counterion and hydration state can influence hygroscopicity, dissolution rate, and long-term stability. Counterion identity is not specified for this item.

What to check on the CoA/Spec Sheet:

• Identity confirmation (HPLC/LC–MS/UV–Vis profile), purity by HPLC, residual solvents, and moisture.
• Performance tests (literature/common): fluorescence enhancement with RNA or oligo standards, background in typical buffers, and stability under recommended storage.
• Bioburden and nuclease testing where relevant to molecular biology workflows.

Practical tips:

• Use nuclease-free materials and buffers to maintain performance for RNA applications.
• Prepare single-use aliquots to avoid freeze–thaw cycles that may affect performance or introduce contamination.

Reaction and Applications

This product is a detection reagent for nucleic acids rather than a synthetic reagent. Accordingly, “reactions” refer to noncovalent binding to nucleic acids and fluorescence reporting.

Applications (literature/general for SYBR Green II-type dyes):

• RNA gel staining: Post-stain polyacrylamide (urea-PAGE) or agarose (formaldehyde/MOPS) gels to visualize rRNA, tRNA, and mRNA. Provides high sensitivity with lower background for single-stranded nucleic acids relative to dsDNA stains.
• Solution assays: Quantification of RNA in microplate or cuvette formats by fluorescence enhancement upon binding.
• Northern blot pre- or post-staining of gels to assess RNA integrity before transfer.
• ssDNA/oligonucleotide visualization in native or denaturing gels.

Practical tips:

• Binding is noncovalent and environment-sensitive; optimize dye concentration to balance sensitivity and background. Excess dye may cause quenching or increased background.
• Minimize exposure to ambient light during staining and imaging to prevent photobleaching.
• For denaturing RNA gels (formaldehyde), ensure adequate rinsing in nuclease-free water or buffer before staining to reduce interference.
• Use compatible filter sets: excitation in blue-green and emission in green; many EtBr filter sets are not optimal—verify instrument settings.

Not typically applicable:

• Grignard/cross-coupling/organometallic reactions are irrelevant for this product; see Application Protocols and Buffer Applications for practical use details.

Reaction Conditions

This section is not typically applicable because the product is a fluorescent dye used for detection rather than a reagent for chemical synthesis. Nevertheless, the following practical conditions relate to staining workflows (literature/general; not item-specific specifications):

• Stock preparation: Commonly dissolved in anhydrous DMSO (light-protected) to make concentrated stocks; aliquot to avoid freeze–thaw. Aqueous nuclease-free stocks are also used for short-term work.
• Post-staining gels: Incubate gels in dilute dye solution with gentle agitation at room temperature, protected from light. Typical times range 10–40 minutes depending on gel thickness and target abundance. Optional brief rinses reduce background.
• Imaging: Blue/green-light transilluminators or laser scanners with excitation in the 480–500 nm range and emission capture around 530–550 nm are commonly employed.
• Solution assays: Equilibrate dye with RNA standards and samples in assay buffer; measure fluorescence after a short incubation (minutes) once signal stabilizes.

Expected performance (general):

• Detection sensitivity is high for RNA/ssDNA with linear dynamic ranges that depend on instrument and buffer. Validate concentration and exposure settings for your setup.

For precise, validated conditions in your laboratory, run small pilot tests to optimize staining time, dye concentration, and imaging parameters.

Safety and Handling

GHS/SDS information for this specific item is not provided below; consult the product SDS for authoritative hazard classifications and response measures.

• Signal Word: Not specified for this item; refer to SDS.
• H-Statements / GHS Classification / Pictograms: Not specified for this item; refer to SDS.

General laboratory safety guidance for nucleic-acid dyes (literature/best practice):

• PPE: Wear lab coat, nitrile gloves, and safety glasses. Change gloves frequently when handling concentrated dye stocks.
• Engineering controls: Work in a well-ventilated area; use a chemical fume hood when preparing concentrated stock solutions, aliquoting, or cleaning spills.
• Avoid exposure: Prevent skin/eye contact and inhalation of aerosols/dust. Many cyanine dyes are biologically active intercalators; handle accordingly.
• Light sensitivity: Protect from light at all times (foil-wrap containers, use amber vials) to prevent photodegradation.
• Incompatibilities: Strong oxidizers and strong acids/bases may degrade the dye; avoid contact with bleach during waste handling unless validated protocols are followed.
• Spill/first aid (overview): For small spills, absorb with inert material, avoid generating dust/aerosol; wash area with detergent. If skin contact occurs, wash with soap and water; for eye exposure, rinse with water for at least 15 minutes and seek medical attention. If inhaled, move to fresh air; if ingested, rinse mouth and seek medical advice.
• Waste: Collect dye-containing solutions as hazardous chemical waste according to institutional and local regulations; do not dispose to drain unless permitted.

Always defer to the SDS and institutional EHS guidance for binding dyes.

Solvent Selection

This product is a fluorescent dye rather than a reaction solvent. Solvent considerations relate to stock preparation and staining performance rather than reaction media.

General guidance (literature/practice):

• Stock solutions: Commonly prepared in anhydrous DMSO to achieve stable, concentrated stocks; water (nuclease-free) may also be used at lower concentrations. Item-specific solvent guidance is not specified for this product.
• Working solutions: Typically diluted into electrophoresis buffers (e.g., TBE/TBE-urea for PAGE; MOPS or formaldehyde/MOPS for RNA agarose gels) or nuclease-free water for solution assays.
• Polarity/miscibility: DMSO and water are fully miscible; transition from DMSO stock to aqueous buffer should be gradual with mixing to avoid local overconcentration that can lead to dye aggregation.
• Additive effects: High salt, detergents, or chaotropes can shift fluorescence response; validate in your assay buffer.

Quick comparison (general, not item-specific):

• DMSO stocks: Higher solubility and stability; protect from moisture and light.
• Aqueous stocks: Convenient for rapid use; shorter shelf-life and greater risk of photobleaching or microbial growth—use sterile, filtered, nuclease-free solutions and store cold/dark.

Avoid:

• Strong acids/bases and oxidants that can degrade cyanine dyes.
• Repeated freeze–thaw of concentrated stocks; aliquot for single-use.

Storage and Reconstitution

Item-specific conditions from Product Data:

• Storage Conditions: Store at -20°C
• Shipped In: Ice chest + Ice pads

Additional guidance (general best practice for nucleic-acid dyes; not item-specific specifications):

• Light protection: Store in amber vials or foil-wrapped containers to minimize photodegradation.
• Aliquoting: Upon first opening, prepare small, single-use aliquots to avoid repeated freeze–thaw cycles and to reduce contamination risk.
• Reconstitution: If provided as a solid, dissolve in anhydrous DMSO (common) or nuclease-free water to prepare a concentrated stock. Mix gently to avoid foaming; filter-sterilize aqueous stocks if required for sensitive workflows.
• Working solutions: Prepare fresh on the day of use in compatible buffers (e.g., TBE, MOPS) or nuclease-free water. Keep solutions on ice and protected from light during experiments.
• Stability: Concentrated DMSO stocks are generally more stable than aqueous stocks when stored at −20°C and protected from light; confirm stability for this item on the CoA/Spec Sheet.
• Freeze–thaw: Avoid repeated cycles; discard aliquots that show precipitate, discoloration, or diminished signal.

Always refer to the product CoA and SDS for definitive storage instructions and compatibility information.

Structure and Identity

SYBR Green II (Ionic form) is a nucleic-acid–binding fluorescent dye, widely used for RNA visualization and quantification in electrophoresis and solution assays. It is supplied for research use only.

• SKU: S1452176
• Product Name: SYBR Green II (Ionic form)
• CAS: 178919-00-1
• Category Path: 全部 / 可售 / 生命科学
• Research Use Note: For research use only
• Molecular Formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular Weight: Not specified for this item; refer to CoA/Spec Sheet.
• SMILES: Not specified for this item; refer to CoA/Spec Sheet.
• InChIKey: Not specified for this item; refer to CoA/Spec Sheet.

Structural features (general/literature):

• SYBR Green II is described in the literature as an asymmetrical cyanine-type dye provided in an ionic (salt) form for water/DMSO solubility.
• Contains extended conjugation and cationic heteroaromatic rings that intercalate or bind within nucleic-acid grooves; exhibits strong fluorescence enhancement upon binding RNA and single-stranded nucleic acids.
• No stereocenters are typically involved; structure is largely planar and delocalized to support high molar absorptivity.

2D structure description (general):

• Two heteroaromatic units connected by a polymethine bridge (conjugated chain), bearing ionic substituents to improve aqueous compatibility; counterion varies depending on salt form (not specified for this item).

Synthetic Utility

Not applicable in the conventional organic synthesis sense. SYBR Green II is a detection reagent and is not typically employed as a substrate, catalyst, or reagent in chemical transformations.

Relevant to analytical/synthetic workflows (general):

• Analytical support: Facilitates tracking and quantification of RNA, oligos, and single-stranded DNA during synthetic biology, nucleic acid synthesis, and purification processes (e.g., PAGE analysis of synthetic oligonucleotides).
• Process monitoring: Enables visualization of nucleic acids in QC steps without resorting to UV-intensive EtBr imaging.

For synthetic chemistry transformations, refer to reagents appropriate to your reaction class. Use this dye post-synthesis for analysis only.

Target Specificity

Item-specific target specificity data (e.g., antigen, epitope, clone/isotype) are not applicable to this dye and are not provided in the Product Data.

General note: In literature, SYBR Green II is described as a fluorescent dye with strong signal enhancement upon binding to RNA and single-stranded nucleic acids; however, no item-specific binding constants or selectivity data are provided here. Refer to primary literature and your internal validation for specificity in your assay context.