DLGAP2 Human Pre-designed siRNA Set A

Cat. No.: D1487330

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

개요

DLGAP2 Human Pre-designed siRNA Set A contains three designed siRNAs for DLGAP2 gene (Human), as well as a negative control, a positive control, and a FAM-labeled negative control. Components DLGAP2 siRNA-1: 5 nmol (HPLC) DLGAP2 siRNA-2: 5 nmol (HPLC) DLGAP2 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

보관 조건

Store at -20°C

배송

Ice chest + Ice pads

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Application Protocols

Item-specific tested applications, recommended dilutions/concentrations, and step-by-step protocols: Not specified for this item; refer to CoA/Spec Sheet.

General workflow guidance for siRNA use (not item-specific)

• Reconstitution: Spin down contents, add nuclease-free water or 1× TE to the desired concentration (e.g., 20–100 µM stocks), mix gently, and incubate 10 minutes on ice to ensure full dissolution. Avoid vigorous vortexing of small volumes.
• Aliquoting: Divide into single-use aliquots to avoid freeze–thaw cycles. Label with concentration and date.
• Complex formation: Dilute siRNA and transfection reagent separately in serum-free medium, combine gently, incubate 10–20 minutes at room temperature, then add to cells.
• Verification: At 24–48 h, quantify mRNA by qRT-PCR; at 48–96 h, assess protein by Western blot or immunostaining. Include appropriate controls.
• Data quality: Use multiple siRNA duplexes targeting distinct regions of DLGAP2 to confirm on-target effects; analyze seed-dependent off-target signatures when feasible.

These steps are illustrative; for definitive instructions specific to SKU D1487330, consult the product’s CoA/Spec Sheet.

Biological Roles

Scope

• This section provides literature context about the biological role of the intended target, DLGAP2, and general principles of RNAi. It does not assert performance or effects of this specific product.

DLGAP2 (literature overview)

• Function: DLGAP2 (SAPAP2/GKAP2) is a postsynaptic density (PSD) scaffold that links PSD-95/DLG family MAGUKs to SHANK proteins, contributing to the structural integrity and signaling architecture of excitatory glutamatergic synapses.
• Localization: Predominantly neuronal, enriched at dendritic spines within PSD complexes.
• Interactions: Binds GK domain of PSD-95 and proline-rich domains of SHANKs, coordinating NMDA/AMPA receptor-associated complexes. Multiple isoforms may fine-tune synaptic organization.
• Pathways: Implicated in synaptic plasticity mechanisms, receptor trafficking, and cytoskeletal coupling through multi-protein assemblies.

RNAi context (general)

• siRNA-mediated gene silencing reduces target mRNA levels via RISC loading and Argonaute-guided cleavage or translational repression, enabling transient loss-of-function studies.

Caveats

• Compensation and redundancy among PSD scaffolds (DLGAP family members) can modulate observed phenotypes. Off-target effects and innate immune sensing of dsRNA are potential confounders; use appropriate controls and innate-immune-silent chemistries when needed.

Item-specific biological activity, validated cell lines, and effect magnitude: Not specified for this item; refer to CoA/Spec Sheet.

Buffer Applications

Item-specific buffer composition: Not specified for this item; refer to CoA/Spec Sheet.

General buffer practices for siRNA handling (not item-specific)

• Stock reconstitution: Commonly in nuclease-free water or 1× TE (10 mM Tris-HCl, 1 mM EDTA, pH 7.5–8.0). TE provides improved stability for long-term storage by chelating divalent cations.
• Working dilutions: Prepare in serum-free Opti-MEM or appropriate cell culture medium immediately before transfection; follow transfection reagent manufacturer instructions.
• RNase control: Use certified RNase-free solutions and consumables; avoid repeated freeze–thaw. Include carrier RNA only if recommended for extremely low concentrations.
• Electrophoresis QC: Native PAGE or agarose with ethidium bromide/sybr dyes can assess duplex integrity; use 1× TBE or TAE buffers. Run at low voltages to limit heating.
• pH and ionic strength: Neutral pH (7–8) and moderate ionic strength (≥50 mM Na+) stabilize duplexes; Mg2+ should be minimized during storage to prevent cleavage, unless required for an assay.

Recipes (illustrative; not item-specific)

• 1× TE, pH 8.0: 10 mM Tris-HCl, 1 mM EDTA in RNase-free water. Filter-sterilize if needed.
• 1× TBE: 89 mM Tris, 89 mM boric acid, 2 mM EDTA; often used for native PAGE of nucleic acids.

Green Alternatives

Applicability

• Green chemistry considerations pertain to the transfection and cell culture workflow rather than the siRNA itself. The product contains no solvent selection data. Below are general, non–item-specific suggestions to reduce environmental and user hazards.

General greener practices for siRNA experiments (literature/guidance)

• Transfection reagents: Prefer biodegradable, serum-compatible lipids/polymers with lower cytotoxicity, reducing waste from failed transfections and minimizing hazardous waste compared with older cationic lipids.
• Solvent minimization: Prepare concentrated aqueous siRNA stocks to reduce packaging and shipping mass; avoid organic cosolvents.
• Plastic reduction: Use multiwell formats and automation-friendly low-dead-volume consumables to minimize plastic waste; select RNase-free but recyclable plastics when feasible.
• Energy efficiency: Store working aliquots at −20°C rather than −80°C when stability allows (this item specifies −20°C), and limit freezer door openings by batching retrievals.

Illustrative comparison (general; not item-specific)

• Conventional cationic lipid (older formulations): Higher cytotoxicity, may require serum-free conditions; more repeats to achieve effect.
• Modern lipid nanoparticles/ionizable lipids: Improved potency in serum, lower dose requirements; check SDS for hazard profile.

Note

• Any specific environmental, safety, or materials disclosures for this catalog item are Not specified; consult the SDS/CoA for definitive information.

Pharmaceutical Uses

This catalog item is designated “For research use only” and is not intended for human or animal therapeutic, diagnostic, or clinical use.

General context (not item-specific; no therapeutic claims)

• In pharmaceutical research, siRNA tools are used for target validation, pathway deconvolution, and screening to support discovery programs. Transient knockdown can help de-risk targets prior to small-molecule or biologic campaigns.
• Manufacturing/process development: Oligonucleotide analytics (A260, HPLC, MS) and formulation learnings from research-grade siRNA can inform later development of GMP-grade materials, though this product itself is not GMP and lacks specified pharmacopeial status.
• Excipients/formulation (research scale): Buffers such as TE and isotonic diluents are commonly employed in vitro. For in vivo or clinical applications, specialized delivery systems and GMP controls are required; these are out of scope for this research-only product.

Item-specific regulatory status, GMP grade, endotoxin/bioburden limits, and pharmacopeial compliance: Not specified for this item; refer to CoA/Spec Sheet.

Physical Properties

Item-specific properties

• Appearance, concentration, salt form, buffer composition: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight (per duplex), exact length, and purity: Not specified for this item; refer to CoA/Spec Sheet.

General/literature properties of siRNA (not item-specific)

• Typical duplex length: 19–27 base pairs with 2-nt 3′ overhangs (literature).
• Approximate molecular mass: ~13–17 kDa per 21-mer duplex depending on sequence and modifications (literature; sequence dependent).
• Solubility: Freely soluble in nuclease-free water and aqueous buffers; insoluble in most organic solvents (literature).
• pKa/logP: Not directly applicable to polyanionic oligonucleotides; behavior governed by multiply ionized phosphate backbone (literature).
• UV properties: Strong absorbance at 260 nm; extinction coefficient sequence dependent (literature). Quantification typically by A260 using strand-specific ε values or mass provided by supplier.
• Thermal behavior: No defined BP/MP. Duplex stability described by melting temperature (Tm), which depends on length, GC content, salt, and chemical modifications (literature).

Handling notes (general)

• Avoid RNase contamination; use RNase-free consumables. Reconstitute to convenient stock (e.g., 10–100 µM) in nuclease-free water or 1× RNase-free TE; exact recommendations for this item are Not specified.

Quality and Grades

Item-specific quality information

• Grade/purity, synthesis method, desalting/HPLC, endotoxin level: Not specified for this item; refer to CoA/Spec Sheet.

How to interpret common siRNA quality attributes (general, not item-specific)

• Purity designation: “Desalted,” “PAGE-purified,” or “HPLC-purified” indicate progressively higher oligo purity. HPLC/PAGE purification reduces n−1/n+1 species and truncated products, improving potency and reproducibility.
• Identity confirmation: Common methods include MALDI-TOF/ESI-MS for average mass, capillary electrophoresis or ion-pair RP-HPLC for purity profile, and UV A260 for quantitation. Sequence verification may use enzymatic digestion MS mapping.
• Modifications: Chemical stabilizations (e.g., 2′-O-Me, 2′-F, terminal phosphorothioates) and overhang composition affect nuclease resistance and immunostimulation. Presence/absence for this item is Not specified.
• Duplex formation: Vendors may supply pre-annealed duplexes or separate sense/antisense strands. Pre-annealing status for this item is Not specified.
• Lot-to-lot documentation: Expect a Certificate of Analysis detailing OD260 or nmol amount, purity (%), residual salts/solvents, and storage buffer if applicable. For this product, refer to CoA/Spec Sheet for definitive values.

Practical note

• For assay-critical work (HTS, phenotypic screening), consider HPLC- or PAGE-purified duplexes with documented endotoxin/bioburden controls when available; confirm what applies to this catalog item via its CoA.

Reaction and Applications

Item-specific manufacturer applications: Not provided in Product Data; refer to CoA/Spec Sheet.

General research applications of pre-designed siRNA (not item-specific)

• Gene silencing via RNA interference: Transient knockdown of DLGAP2 transcripts in human cells to probe pathway function, assess phenotypic outcomes, or validate targets. Use in forward and reverse genetics, and as controls in CRISPR studies.
• Screening: Sets (“Set A”) often include multiple non-overlapping duplexes to mitigate off-targets and confirm on-target effects through concordant phenotypes.
• Mechanistic notes: The guide strand is loaded into RISC; Argonaute-mediated endonucleolytic cleavage or translational repression occurs at complementary mRNA.
• Controls: Combine with non-targeting siRNA, positive knockdown controls, and rescue experiments (siRNA-resistant cDNA) to strengthen conclusions.
• Readouts: qRT-PCR for mRNA reduction, Western blot for protein knockdown, RNA-seq for transcriptome-wide effects, and functional assays appropriate to neuronal/synaptic biology when studying DLGAP2.

Practical considerations

• Transfection optimization (cell line dependent): Reagent choice, siRNA dose (e.g., 1–50 nM typical, literature), cell density, and exposure time (24–96 h) greatly affect outcomes. Titrate to minimize cytotoxicity while maximizing knockdown.
• Off-target minimization: Pooling low-dose duplexes, using validated designs, and applying seed control analyses reduce seed-mediated effects (literature guidance).

Reaction Conditions

Not a chemical reaction reagent in the conventional sense. However, functional use depends on transfection and cell culture conditions. No item-specific conditions are provided in the Product Data.

General literature guidance for siRNA transfection (not item-specific)

• Cell density: 30–70% confluency at transfection is typical; optimize per cell line.
• Dose: 1–50 nM final siRNA is a common screening range; lower doses with pooled duplexes can reduce off-targets.
• Media: Use serum-free medium during complex formation for many lipid reagents; many modern reagents tolerate serum during transfection—follow reagent instructions.
• Incubation: 4–6 h complex exposure followed by media change, or continuous exposure for low-toxicity reagents. Assess knockdown at 24–96 h (mRNA early; protein later).
• Controls: Non-targeting siRNA, positive control siRNA (against a housekeeping gene), and transfection-only controls are essential.
• Readouts: qRT-PCR, Western blot, reporter assays.

Item-specific recommended reagent, timing, or performance metrics: Not specified for this item; refer to CoA/Spec Sheet.

Safety and Handling

Item-specific safety details

• GHS classification, pictograms, signal word, H-statements: Not specified for this item; refer to SDS.
• Research use note: For research use only (per Product Data).
• Storage condition (per Product Data): Store at −20°C. Shipped in ice chest with ice pads.

General guidance for siRNA/oligonucleotides (not item-specific; consult SDS for authoritative info)

• Expected hazards: Synthetic siRNA duplexes are generally considered low hazard. Primary risks arise from dust/aerosol generation and potential irritation. Avoid inhalation, ingestion, and contact with eyes or skin.
• PPE: Lab coat, gloves (change frequently to control RNase), and safety glasses. Work in a clean area; for lyophilized materials, open carefully to avoid loss and aerosolization.
• RNase control: Use RNase-free tubes/tips; wipe benches and tools with RNase decontamination solutions. Avoid touching tube rims and inside caps.
• Incompatibilities: Strong nucleases (RNases), extreme pH (<5 or >9) over extended time, and repeated freeze–thaw cycles can degrade RNA. Avoid microbial contamination.
• First aid (general): If contact with eyes/skin, rinse with water. If inhaled, move to fresh air. If ingested, rinse mouth. Seek medical attention if symptoms occur. Provide SDS to healthcare personnel.
• Waste: Dispose of RNA-containing solutions in accordance with institutional biosafety and local regulations; decontaminate surfaces with appropriate agents.

Solvent Selection

Applicability to this product

• siRNA duplexes are aqueous biomolecules; organic solvent selection is generally not relevant. Focus is on nuclease-free aqueous media.

General guidance for siRNA dissolution (not item-specific)

• Primary solvents: Nuclease-free water (RNase/DNase-free), 1× TE (10 mM Tris-HCl, 1 mM EDTA, pH 7.5–8.0), or 1× siRNA resuspension buffers provided by vendors.
• pH/ionic strength: Neutral to slightly basic pH (7.0–8.0) supports stability; low millimolar EDTA can chelate trace metal ions that catalyze degradation.
• Cosolvents: Avoid alcohols and most organic solvents; they reduce solubility and can precipitate RNA. If mixing with transfection formulations, follow reagent vendor guidance.
• Sterility: Filter sterilization is typically unnecessary for oligos supplied sterile; if required, use low-protein-binding 0.22 µm filters and minimize shear.

When to choose buffer vs water (general)

• Water: Best for short-term use, downstream enzymology, or when EDTA could interfere with Mg2+-dependent processes.
• TE buffer: Preferred for stock solutions intended for longer storage; EDTA sequesters divalent cations that promote hydrolysis.

Item-specific solvent/buffer recommendations, concentrations, and annealing status: Not specified for this item; refer to CoA/Spec Sheet.

Storage and Reconstitution

Item-specific storage and shipping (from Product Data)

• Storage: Store at −20°C.
• Shipping: Shipped in ice chest with ice pads.

Item-specific details not provided

• Supplied form (lyophilized vs. in solution), buffer composition, initial concentration, and stabilizers: Not specified for this item; refer to CoA/Spec Sheet.

General best practices for siRNA (not item-specific)

• Upon receipt: If lyophilized, equilibrate to room temperature in a desiccator before opening to prevent condensation. Briefly centrifuge to collect material.
• Reconstitution: Use nuclease-free water or 1× TE (pH 7.5–8.0). Typical stock concentrations are 20–100 µM. Mix gently and allow 10 minutes for full dissolution on ice.
• Aliquoting and storage: Prepare single-use aliquots; store at −20°C (short-to-medium term) or −80°C (long term) in low-adsorption tubes. Protect from repeated freeze–thaw cycles and from RNases.
• Stability notes: Avoid prolonged exposure to room temperature, extreme pH, or divalent cations. For solutions, minimize headspace and consider layering with RNase-free argon if long-term storage is required.
• Thawing: Thaw on ice, mix by gentle flicking/low-speed vortex, and quick spin to collect. Keep on ice during setup.

Always defer to the product-specific CoA/SDS for definitive storage, stability, and reconstitution guidance.

Structure and Identity

Item-specific facts (from Product Data)

• Product: DLGAP2 Human Pre-designed siRNA Set A (SKU: D1487330)
• Intended target: Human DLGAP2 mRNA (gene symbol inferred from product name); exact sequences, duplex count, and modifications: Not specified for this item; refer to CoA/Spec Sheet.
• CAS, CID, InChIKey, SMILES, empirical formula, average molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

General/literature description of siRNA structure (not item-specific)

• Typical siRNA format: 19–21 bp double-stranded RNA with 2-nt 3′ overhangs (e.g., dTdT), antiparallel strands with Watson–Crick base pairing.
• Backbone: Repeating ribose–phosphate (phosphodiester or phosphorothioate if modified) with nucleobases A, U, G, C. Chemical stabilizations (2′-O-Me, 2′-F, terminal phosphorothioates) may be used in some products to enhance nuclease resistance; presence/absence here is Not specified.
• 2D description in words: Two complementary ribonucleotide strands aligned in antiparallel orientation, each bearing 5′ phosphate or hydroxyl and 3′ hydroxyl (or overhangs), forming an A-form helix upon annealing; recognition by RISC after loading of the guide strand.

Context on target (literature)

• DLGAP2 (Discs large-associated protein 2, aka SAPAP2/GKAP2) encodes a postsynaptic density scaffold interacting with PSD-95/DLG and SHANK families, organizing excitatory synaptic signaling complexes in neurons. No claim is made about biological effects of this specific siRNA set.

Synthetic Utility

Not typically applicable. This product is a pre-designed siRNA duplex set intended for biological knockdown studies, not a small-molecule building block or synthetic reagent.

General note (contextual)

• While oligonucleotides can serve as templates or primers in enzymatic synthesis, research siRNA duplexes are not used as reagents in traditional organic synthesis or catalysis. For chemical biology, they may be substrates in ligation or labeling reactions (e.g., click-ready modifications), but any such modifications for this item are Not specified.

Target Specificity

From Product Data

• Target: Human DLGAP2 (as stated in product name: DLGAP2 Human Pre-designed siRNA Set A).
• Format: Pre-designed siRNA set (“Set A”); number of duplexes, sequences, and any chemical modifications: Not specified for this item; refer to CoA/Spec Sheet.

Not provided in Product Data

• Validated cell lines, knockdown efficiency, off-target assessment, and cross-reactivity information: Not specified for this item; refer to CoA/Spec Sheet.