AGPS Human Pre-designed siRNA Set A

Cat. No.: A1487283

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Panoramica

AGPS Human Pre-designed siRNA Set A contains three designed siRNAs for AGPS gene (Human), as well as a negative control, a positive control, and a FAM-labeled negative control. Components AGPS siRNA-1: 5 nmol (HPLC) AGPS siRNA-2: 5 nmol (HPLC) AGPS siRNA-3: 5 nmol (HPLC) siRNA Negative Control: 5 nmol (HPLC) FAM-labeled siRNA Negative Control: 5 nmol (HPLC) GAPDH siRNA Positive Control:5 nmol (HPLC)

Specifications

Condizioni di conservazione di stoccaggio

Store at -20°C

Spedito in

Ice chest + Ice pads

Questo prodotto richiede spedizione a catena fredda. I servizi di terra e altri servizi economici non sono disponibili.

Product Line

biological_products

Application Protocols

• Item-specific tested applications and dilutions: Not specified for this item; refer to CoA/Spec Sheet.

• General transfection workflow for siRNA (literature guidance; adjust per cell line/reagent)

  1. Thaw siRNA and transfection reagent on ice. Mix gently.
  2. Prepare siRNA stock in RNase-free water/TE (e.g., 20–100 µM). For working complexes, dilute siRNA in serum-free medium (e.g., Opti-MEM) to achieve 1–50 nM final in wells.
  3. In a separate tube, dilute transfection reagent in the same medium. Incubate 5 min.
  4. Combine diluted siRNA and reagent; incubate 10–20 min at room temperature to allow complex formation.
  5. Add complexes to cells at 40–80% confluence. Optionally replace medium after 4–6 h, depending on reagent tolerance.
  6. Assay knockdown: mRNA by qRT-PCR at 24–48 h; protein by immunoblotting at 48–96 h, depending on protein turnover.
  7. Include controls: non-targeting siRNA, positive control siRNA, and mock-transfected cells.

• Troubleshooting tips

  • Low knockdown: Optimize dose, reagent ratio, and cell density; verify RNA integrity and target expression.
  • Cytotoxicity: Reduce siRNA and/or reagent amounts; switch to gentler transfection reagents; shorten exposure.
  • Off-target effects: Use multiple siRNAs, pooled designs, and minimal effective concentrations.

Biological Roles

• Item-specific target

  • Target gene: AGPS (alkylglycerone phosphate synthase), human (from product name). This enzyme localizes to peroxisomes.

• General biology (literature; not item-specific claims)

  • AGPS function: Catalyzes the formation of alkylglycerone phosphate, a key step in ether lipid (plasmalogen) biosynthesis within peroxisomes.
  • Pathway context: Ether lipids contribute to membrane architecture, redox homeostasis, and signaling lipid pools; AGPS knockdown can perturb plasmalogen levels and downstream lipid pathways in cells.
  • Cellular impact: Suppression of AGPS expression is commonly used to probe peroxisomal lipid metabolism, membrane dynamics, and associated biochemical phenotypes in model systems.

• RNAi mechanism (literature)

  • siRNA duplexes are processed by RISC; the guide strand directs sequence-specific cleavage of complementary AGPS mRNA, reducing translation and protein levels.
  • On-target validation: Employ multiple siRNA sequences, rescue experiments with siRNA-resistant AGPS cDNA, and orthogonal tools (e.g., CRISPRi) to confirm specificity.

Note: All uses are for research in vitro/in cellulo studies; no clinical, diagnostic, or therapeutic claims are made for this product.

Buffer Applications

This product is an siRNA reagent and is not a classical buffer. However, appropriate buffers are essential for stability and performance.

• Item-specific details

  • Supplied buffer/composition: Not specified for this item; refer to CoA/Spec Sheet.

• General guidance (literature)

  • Reconstitution: Use RNase-free water or 1× TE (10 mM Tris-HCl, 1 mM EDTA, pH 7.5–8.0). EDTA chelates divalent cations that catalyze RNA hydrolysis, improving stability.
  • Working dilutions: Prepare in nuclease-free 1× buffer compatible with the transfection reagent and cell culture medium; avoid excessive ionic strength that can affect complexation.
  • Storage aliquots: Small-volume aliquots in TE help reduce adsorption to plastics and freeze–thaw stress.

• Electrophoresis/analysis

  • For quality checks, native or denaturing PAGE in TBE/urea systems can assess integrity; stain with RNA-compatible dyes. This is optional for pre-validated siRNAs and not item-specific.

Because this is a functional gene-silencing reagent, focus on nuclease-free, mildly buffered aqueous solutions rather than on specialized buffer systems.

Green Alternatives

Although this product is an aqueous oligonucleotide reagent, greener practices can be applied to its handling and use.

• Solvent and reagent considerations (general)

  • Prefer RNase-free water or TE buffer for reconstitution and dilution—these are inherently benign compared with organic solvents.
  • Reduce or eliminate chloroform/phenol extraction steps; use column-based RNA prep/analysis where possible.
  • Choose transfection reagents with lower cytotoxicity and biodegradable components when feasible; evaluate supplier green profiles.

• Process efficiency

  • Work at higher stock concentrations (within solubility limits) to reduce plastic consumables and cold-chain volume.
  • Implement miniaturized transfection formats (96–384-well) to lower reagent consumption and waste.

• Decontamination and waste

  • Use non-halogenated RNase decontamination solutions where effective.
  • Segregate aqueous nucleic-acid waste; avoid unnecessary solvent rinses.

• Comparison snapshot (general; not item-specific)

  • Conventional approach: Ethanol precipitation, phenol–chloroform steps, solvent-heavy workflows.
  • Greener approach: Direct aqueous handling, spin-column cleanups, and minimized plasticware via automation/miniaturization.

Adopting these practices reduces environmental footprint without compromising siRNA performance.

Pharmaceutical Uses

• Item-specific regulatory status

  • For research use only. No pharmacopeial monographs or clinical formulation status are provided for this item.

• General context (literature; not a claim for this product)

  • siRNA molecules are widely used in discovery and preclinical research for target validation, pathway interrogation, and mechanism-of-action studies that inform therapeutic programs.
  • Formulation concepts for siRNA therapeutics include LNPs, conjugates (e.g., GalNAc), and polymeric carriers; these are not applicable to this research-use product unless explicitly stated.

• Handling in translational research settings

  • Where formulation-like studies are performed in vitro, ensure extremely low endotoxin levels and well-characterized purity; such specifications are not provided for this item and should not be assumed.

No clinical, diagnostic, or therapeutic use is intended or implied for this product.

Physical Properties

• Item-specific properties

  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet. (For siRNA, MW depends on sequence length and modifications.)
  • Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
  • Solubility: siRNAs are typically soluble in RNase-free water or low-ionic-strength buffers (e.g., TE); item-specific solubility not specified.
  • Other specifications (UV cutoff, ε, purity by HPLC, water content): Not specified for this item; refer to CoA/Spec Sheet.

• General/literature values for siRNA (for planning only; not item specs)

  • Typical length: 19–27 bp duplex with 2-nt 3' overhangs.
  • Solubility: readily soluble to ≥100 µM in RNase-free water or 1× TE (10 mM Tris, 1 mM EDTA), pH 7.0–8.0.
  • Extinction coefficient: sequence-dependent; can be calculated from nearest-neighbor parameters; measure A260 for concentration (literature).
  • Physical state: supplied lyophilized or in aqueous buffer; rehydrate in RNase-free water (literature). Actual form for this product is not specified.

Note: Boiling point, melting point, density, logP, pKa, refractive index are not typically applicable/defined for macromolecular oligonucleotide mixtures; not specified for this item.

Quality and Grades

• Item-specific quality

  • Grade/purity: Not specified for this item; refer to CoA/Spec Sheet.
  • Sequence disclosure, modification profile, residual salts/solvents, and HPLC traces: Not specified for this item; refer to CoA/Spec Sheet.

• General guidance on siRNA quality (literature/industry practice)

  • Desalted vs. HPLC-purified: HPLC purification reduces truncated sequences and improves knockdown consistency—often preferred for demanding applications. Desalted material may suffice for robust cell lines and screening.
  • Modification grade: Chemical modifications (e.g., 2'-O-Me, 2'-F, phosphorothioate caps) can improve nuclease resistance and in vivo stability; confirm modification details on the CoA if present.
  • UV purity and ID: OD260 measurement and calculated extinction coefficients confirm concentration; LC/MS (if provided) confirms molecular mass.
  • Endotoxin/bioburden: For sensitive primary cells or in vivo studies, low endotoxin specifications may be critical; verify if relevant. Not specified for this item.

• Implications for use

  • Higher-purity siRNA often yields more reproducible gene silencing and lower off-target effects; however, follow the manufacturer’s guidance for the intended application scope of this specific set.

Always consult the item’s CoA/Spec Sheet for definitive grade, purity, and analytical data.

Reaction and Applications

As an siRNA reagent, this product is intended for sequence-specific gene silencing via the RNA interference (RNAi) pathway in cultured cells or other experimental systems.

• Item-specific application note

  • Manufacturer Applications: Not specified beyond product name; typical use is knockdown of human AGPS expression for research purposes.

• General applications (literature/guidance; not item-specific specs)

  • Gene knockdown: Transient suppression of AGPS mRNA to study gene function, pathway dependency, lipid metabolism impacts, and target validation.
  • Phenotypic screens: Use in loss-of-function screening panels to assess sensitivity to AGPS depletion.
  • Mechanism: Duplex siRNA is incorporated into RISC; the antisense strand guides Ago2-mediated cleavage of complementary AGPS mRNA (literature).
  • Controls: Include non-targeting siRNA controls, positive knockdown controls, and, where possible, multiple independent siRNA sequences to confirm on-target effects.

• Practical tips

  • Optimize transfection conditions (reagent choice, cell density, siRNA dose) to balance efficacy and cytotoxicity.
  • Validate knockdown by qRT-PCR (mRNA) and by immunoblotting or activity assay (protein), ideally at 24–72 h post-transfection, as appropriate for AGPS expression dynamics.
  • Minimize off-target effects by keeping final siRNA concentration as low as achieves robust silencing (often 1–50 nM in mammalian cells, literature guidance).

Reaction Conditions

Conventional reaction-condition guidance (solvent, catalyst, temperature) is not applicable to siRNA as a synthetic reagent.

• General experimental conditions for use (literature; not item-specific specs)
  • Cell culture transfection: Typical final siRNA concentration 1–50 nM; incubate complexes formed with lipid/polymeric transfection reagents per vendor guidance (usually 10–30 min complexation), add to cells at 40–80% confluence, assess knockdown 24–72 h post-dose.
  • Nuclease considerations: Maintain RNase-free conditions; avoid extended exposure to 37°C outside cells. Keep siRNA on ice during setup when feasible.
  • Thermal handling: Briefly heat stocks (e.g., 65°C for 5 min) to resolve secondary structure only if recommended; not routinely required and not specified for this item.

For precise conditions, optimize empirically for each cell type and transfection reagent. Consult the CoA/Spec Sheet for any item-specific instructions if available.

Safety and Handling

• Item-specific hazard information

  • Signal word: Not specified for this item; refer to SDS.
  • H-statements/GHS classification/Pictograms: Not specified for this item; refer to SDS.
  • Research use: For research use only.

• General laboratory safety for siRNA and nucleic acids (literature/guidance)

  • Handle using RNase-free technique: wear clean gloves, use RNase-free tubes/tips, and avoid contacting surfaces that may introduce RNases.
  • PPE: lab coat, gloves, safety glasses. Avoid aerosol generation during reconstitution and transfection mix preparation.
  • Incompatibilities: Avoid strong oxidants, nucleases (RNases), and microbial contamination. Maintain solutions in clean, nuclease-free buffers.
  • First aid (general): If skin/eye contact with buffers occurs, rinse with water. If inhaled as dried powder/aerosol, move to fresh air. If ingested, rinse mouth with water. Seek medical attention as needed. Always defer to SDS for authoritative guidance.
  • Waste: Dispose of siRNA solutions and transfection mixtures as laboratory chemical/biological waste per institutional procedures. Deactivate RNases on surfaces with appropriate agents (e.g., RNase decontamination solutions).

• Shipping/temperature considerations

  • Shipped in ice chest with ice pads to maintain cool temperature; store at −20°C upon receipt to minimize hydrolysis and nuclease degradation.

Solvent Selection

This product is an oligonucleotide (siRNA) and is not used as an organic solvent.

• Item-specific guidance

  • Recommended solvent for reconstitution: Not specified for this item; refer to CoA/Spec Sheet.
  • General practice (literature): Reconstitute in nuclease-free water or 1× TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5–8.0) to a convenient stock concentration (e.g., 10–100 µM) to minimize adsorption and degradation.

• Miscibility/polarity (contextual)

  • siRNAs are highly polar polyanions; they are soluble in aqueous buffers and insoluble in nonpolar organic solvents. Avoid alcohol precipitation unless concentrating or desalting intentionally; residual ethanol/isopropanol can impair transfection.

• Choosing buffers

  • Use RNase-free, low-salt buffers for stock solutions. Avoid divalent cations (e.g., Mg2+, Ca2+) unless the application specifically requires them, as they may promote RNA hydrolysis.

For practical use, focus on transfection-optimized aqueous media and complexation with transfection reagents rather than organic solvent selection.

Storage and Reconstitution

• Item-specific storage and shipping

  • Storage conditions: Store at −20°C (from Product Data). Avoid repeated freeze–thaw cycles.
  • Shipped in: Ice chest with ice pads (from Product Data). Upon receipt, promptly transfer to −20°C.

• Stability (item-specific)

  • Shelf life and stability data: Not specified for this item; refer to CoA/Spec Sheet.

• Reconstitution (general/literature guidance; not item-specific specs)

  • Use RNase-free water or 1× TE buffer to reconstitute to a convenient stock (e.g., 20–100 µM). Vortex briefly and spin down; allow 10–15 min to fully dissolve.
  • Prepare small aliquots to avoid multiple freeze–thaw events. Store aliquots at −20°C (short-to-mid term). For longer-term storage, −80°C is commonly used.
  • Avoid repeated freeze–thaw cycles; thaw on ice and keep solutions cold during setup. To improve adsorption recovery, include 0.1 mM EDTA or use low-binding tubes.

• Working solution handling

  • Keep working dilutions at 4°C for same-day use; discard after 1–2 days or per internal QC policy.
  • Protect from nucleases: Use RNase-free consumables and decontaminate work surfaces with RNase inactivating solutions.

Always consult the CoA/Spec Sheet for any product-specific reconstitution volumes, buffer composition, and stability data.

Structure and Identity

Brief description: This product is a pre-designed small interfering RNA (siRNA) set targeting the human AGPS gene (alkylglycerone phosphate synthase), supplied for research use.

• Item-specific (from Product Data)

  • Product name: AGPS Human Pre-designed siRNA Set A (SKU: A1487283)
  • Target species: Human (inferred from product name)
  • Storage: Store at −20°C; shipped in ice chest with ice pads
  • CAS, CID, InChIKey, SMILES: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular formula, Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

• Structural features (general/literature for siRNA)

  • Double-stranded RNA duplex, typically 19–27 base pairs with 2-nt 3' overhangs (e.g., dTdT) for efficient RISC loading (literature).
  • Phosphodiester or modified phosphorothioate backbones may be used; base or sugar modifications (e.g., 2'-O-Me, 2'-F) can enhance stability (literature). Specific modifications for this item are not specified.
  • No stereogenic centers in canonical ribonucleotide backbones; sequence-dependent identity is defined by nucleotide order (literature).

• Identity definition for siRNA reagents (general)

  • The primary identifiers are oligonucleotide sequences of sense/antisense strands and any chemical modifications. These are not provided here; consult the CoA/Spec Sheet for exact sequences if applicable.

Synthetic Utility

Not applicable. This product is a biological oligonucleotide (siRNA) designed for gene silencing and is not employed as a synthetic building block or reagent in organic synthesis.

• Guidance
  • For chemical biology, siRNAs can be combined with small molecules to study genetic–chemical interactions, but they do not participate as reagents in named organic reactions.
  • If chemical modification of siRNAs is of interest (e.g., conjugation, labeling), specialized chemistries (NHS esters for amines, click chemistry on azide/alkyne handles) are used on pre-functionalized oligos; modification details for this item are not specified.

Target Specificity

• Item-specific (from Product Data)

  • Target: Human AGPS (alkylglycerone phosphate synthase), inferred from product name “AGPS Human Pre-designed siRNA Set A”.
  • Additional details such as individual siRNA sequences, number of duplexes in the set, off-target minimization strategy, and validation data: Not specified for this item; refer to CoA/Spec Sheet.

• General considerations (literature)

  • Specificity in RNAi is driven by antisense strand complementarity to the target mRNA; seed region (nt 2–8) can cause off-target effects if not carefully designed.
  • Use multiple non-overlapping siRNAs against AGPS and concordant phenotypes to strengthen specificity claims; rescue with siRNA-resistant AGPS cDNA where feasible.