PSMD13 Human Pre-designed siRNA Set A

Cat. No.: P1479901

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

개요

PSMD13 Human Pre-designed siRNA Set A contains three designed siRNAs for PSMD13 gene (Human), as well as a negative control, a positive control, and a FAM-labeled negative control. Components PSMD13 siRNA-1: 5 nmol (HPLC) PSMD13 siRNA-2: 5 nmol (HPLC) PSMD13 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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Product Line

생물 제품

Application Protocols

The following is a generalized workflow for transfecting mammalian cells with siRNA targeting PSMD13. Adjust to your cell type and transfection reagent. These are literature‑based guidelines; they are not item‑specific.

1. Preparation

• Thaw an aliquot on ice. Briefly spin to collect contents. Work RNase‑free.
• Reconstitute to 20–50 µM in RNase‑free water or TE. Vortex gently and incubate 10 min to fully dissolve.

2. Complex formation (example for a 24‑well plate)

• Dilute siRNA in 50 µL serum‑free medium (e.g., Opti‑MEM) to reach a final well concentration of 5–25 nM.
• In a separate tube, dilute transfection reagent per manufacturer instructions.
• Combine, mix gently, and incubate 10–15 min at room temperature.

3. Transfection

• Add complexes dropwise to cells at 30–60% confluence in 400–500 µL complete medium (or replace medium after 4–6 h if required by the reagent).
• Optional: Pool multiple PSMD13‑targeting duplexes at equal molar ratios while keeping total siRNA at the same final concentration.

4. Assay timeline

• 24–48 h: Extract RNA for RT‑qPCR to assess PSMD13 mRNA.
• 48–96 h: Harvest protein for immunoblot; monitor viability and proteasome activity markers.

5. Controls

• Non‑targeting siRNA control, positive knockdown control, and mock transfection.

6. Data quality

• Normalize to housekeeping genes for qPCR; include loading controls for immunoblot; replicate across ≥3 biological replicates.

Biological Roles

Target gene context (general literature):

• PSMD13 encodes a non‑ATPase subunit (often referred to as RPN9) of the 19S regulatory particle within the 26S proteasome. The 19S cap recognizes ubiquitinated substrates, unfolds them, and translocates polypeptides into the 20S core for proteolysis.
• PSMD13 participates in the assembly and structural stability of the 19S lid, influencing substrate processing efficiency and proteostasis.
• Perturbation of PSMD13 levels can impact protein turnover, cell cycle progression, stress responses (e.g., unfolded protein response), and signaling pathways regulated by proteasomal degradation.

Relevance of RNAi against PSMD13 (general):

• siRNA‑mediated reduction of PSMD13 allows functional dissection of proteasome regulatory mechanisms, mapping dependencies in ubiquitin–proteasome pathways, and evaluating compensation within proteasome subunit networks.
• In model systems, knockdown can sensitize cells to proteotoxic stress or alter turnover of short‑lived regulatory proteins, providing mechanistic insights.

Notes and caveats:

• Proteasome subunits are often essential for viability in proliferating cells; partial knockdown strategies (lower doses or transient exposure) may be necessary to observe mechanistic effects without overwhelming cytotoxicity.
• Secondary effects from global proteasome impairment (e.g., accumulation of polyubiquitinated proteins) should be controlled by time‑course studies and orthogonal validation (rescue by siRNA‑resistant PSMD13 constructs, where applicable).

Buffer Applications

This product is not a classical buffering reagent. However, buffer choice is critical for siRNA stability and transfection performance.

• Reconstitution (general guidance): RNase‑free water or TE buffer (10 mM Tris‑HCl, 0.1–1 mM EDTA, pH 7.5–8.0). EDTA chelates divalent cations that catalyze RNA hydrolysis.
• Working stocks: 10–50 µM in RNase‑free water or low‑salt buffer to facilitate accurate pipetting. Store aliquots at −20 °C per Product Data.
• Transfection complex formation: Many lipid reagents recommend complexing siRNA in low‑salt, serum‑free medium (e.g., Opti‑MEM) for 5–20 min before adding to cells; then dilute into complete medium as directed (follow reagent‑specific IFU).
• pH range: Near‑neutral (pH 7.0–8.0) conditions preserve ribose 2′‑OH integrity and reduce base‑catalyzed transesterification (literature).
• Avoid: RNase contamination; repeated freeze–thaw; high Mg2+ without chelators during storage; strong acids/bases.

Quick recipe examples (literature):

• TE, pH 7.5: 10 mM Tris‑HCl + 0.1 mM EDTA in RNase‑free water; filter‑sterilize and DEPC‑treat if appropriate for your facility.
• siRNA reconstitution water: Molecular biology‑grade, nuclease‑free; optionally include 1 mM sodium citrate (pH ~6.5) to improve stability during lyophilized cake dissolution.

Green Alternatives

Conventional “green chemistry” frameworks are less directly applicable to biological oligonucleotide reagents. Nonetheless, several practices can reduce environmental impact while maintaining experimental quality:

• Reduce reagent use via optimization: Pilot a small matrix of siRNA concentrations (e.g., 5–10–20 nM, literature) to find the minimum effective dose, lowering upstream manufacturing footprint and plastic waste.
• Favor low‑toxicity, serum‑compatible transfection reagents to minimize repeat experiments and waste generation.
• Consolidate experiments with pooled siRNA duplexes targeting PSMD13 to achieve robust knockdown at lower per‑duplex concentrations (general practice; not item‑specific).
• Use reusable, RNase‑free aluminum cold blocks instead of large volumes of single‑use ice where feasible.
• Dispose of nucleic acid waste via institutional pathways; avoid bleach with high organic loads where alternatives (e.g., RNase inactivating agents) suffice.

Comparison of delivery approaches (general considerations):

• Lipid‑based transfection: Widely applicable; moderate cytotoxicity risk; minimal specialized equipment.
• Polymer‑based reagents: Cost‑effective; variable toxicity; may generate more plastic waste due to optimization.
• Electroporation: No chemical carriers; higher energy input; often higher cell mortality; suited for hard‑to‑transfect cells, potentially reducing repeat attempts.

Pharmaceutical Uses

This is a research‑grade gene‑silencing reagent and is not intended for therapeutic or diagnostic use.

• Pharmacopeial status: Not applicable; no compendial monograph is indicated.
• Formulation/excipient role: Not applicable. The siRNA is intended for in vitro cell biology and molecular biology experiments, not for incorporation into clinical dosage forms.
• Manufacturing context: If adapted for preclinical workflows, users typically ensure low endotoxin levels and stringent documentation; such specifications are Not specified for this item; refer to CoA/Spec Sheet.

Note: All experimental use should comply with institutional biosafety guidelines for handling recombinant/synthetic nucleic acids and transfection reagents.

Physical Properties

Item-specific physicochemical constants are not provided for this siRNA set. Typical properties for siRNA duplexes are summarized for context; these are literature/general values and not specifications for this item.

• Appearance: Not specified for this item; refer to CoA/Spec Sheet. (Commonly delivered lyophilized or in aqueous RNase‑free solution.)
• Molecular weight: Not specified for this item. (Literature: a 21‑mer duplex is ~13–14 kDa; exact MW depends on length/base composition and any modifications.)
• Solubility: High in RNase‑free water and low‑salt buffers (e.g., TE or 1× siRNA buffer, literature). Insoluble in organic solvents.
• pKa / logP: Not applicable in the conventional sense for large, polyanionic oligonucleotides.
• UV absorbance: Strong absorption at 260 nm (literature). Extinction coefficient depends on sequence; Not specified for this item; refer to CoA/Spec Sheet.
• Thermal properties (literature): Duplex melting temperature (Tm) typically 55–85 °C for 19–23 bp under physiological ionic strength; exact Tm is sequence‑dependent.
• Refractive index / density / BP / MP: Not applicable or not meaningful for lyophilized/aqueous oligonucleotide preparations.

Practical notes (general):

• Reconstitute to 10–50 µM in RNase‑free water or buffer for convenient handling (literature guidance).
• Quantify concentration by A260 using a sequence‑specific extinction coefficient when available from the CoA.

Quality and Grades

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

Interpretation and typical expectations (general literature/practice; not specifications for this item):

• siRNA oligos are commonly provided desalted or HPLC‑purified. HPLC purification reduces truncated sequences and improves knockdown consistency, especially at lower working doses.
• Duplex annealing quality and strand stoichiometry can impact potency; some suppliers provide annealed duplexes with verified equimolarity.
• Identity/Quality Controls often include MALDI‑TOF/ESI mass confirmation of single strands, UV A260 quantitation, and endotoxin testing for sensitive primary cells. These controls are not specified for this item; consult the CoA.
• Stabilizers/format: Lyophilized siRNA may include volatile counterions (e.g., Na+) and trace buffering salts to aid stability; solution formats may include RNase‑free water or low‑ionic strength buffer. Not specified for this item.

What matters for experimental quality:

• Sequence design (multiple non‑overlapping duplexes) and inclusion of appropriate controls (non‑targeting, positive knockdown controls).
• Purity and absence of nuclease contamination.
• Batch documentation (CoA) for mass confirmation, concentration, and recommended handling.

Reaction and Applications

This siRNA set is intended for sequence‑specific post‑transcriptional gene silencing of human PSMD13 via the RNA interference (RNAi) pathway.

Applications (general, literature):

• Transient knockdown of PSMD13 in human cell lines to study proteasome function, protein turnover, and stress responses.
• Pathway mapping and target validation in ubiquitin–proteasome system research, including synthetic lethality screens with proteasome inhibitors.
• Phenotypic assays: cell cycle, proteostasis, autophagy crosstalk, unfolded protein response.
• Omics integration: RNA‑seq or proteomics following knockdown to define PSMD13‑dependent networks.

Mechanistic notes (general):

• The antisense (guide) strand loads into RISC, directing Argonaute‑mediated cleavage of complementary PSMD13 mRNA, reducing transcript and protein levels.
• Pooling multiple non‑overlapping siRNAs can increase knockdown robustness and reduce off‑target effects by lowering the concentration of each duplex.

Practical tips:

• Validate knockdown at mRNA level by RT‑qPCR (24–48 h) and protein level by immunoblot (48–96 h), as proteasome subunits can be long‑lived.
• Use appropriate controls: non‑targeting siRNA, positive control siRNA (e.g., PLK1 in proliferating cells), and mock transfection.
• Optimize transfection conditions per cell type: delivery reagent, cell density, serum conditions, and siRNA dose (typical 5–50 nM final, literature).
• Minimize innate immune activation by using serum‑compatible reagents and avoiding excessive siRNA concentrations; consider modified siRNAs if necessary (not specified for this item).

Reaction Conditions

Conventional chemical reaction parameters (solvent, catalysts, yields) do not apply. The relevant “conditions” are for transfection and gene silencing in cell culture (general, literature guidance; not item‑specific):

• Cell density: Plate to reach ~30–70% confluence at transfection.
• Complex formation: Mix siRNA (final 5–50 nM) with transfection reagent in serum‑free medium; incubate 5–20 min to allow complexation.
• Incubation: Add complexes to cells; incubate 4–6 h before replacing with complete medium if required by the reagent, or leave in if serum‑compatible.
• Temperature/Atmosphere: 37 °C, 5% CO2 for mammalian cells.
• Timeline: mRNA reduction typically detectable at 24–48 h; protein reduction at 48–96 h depending on protein half‑life.
• Replicates/controls: Include non‑targeting siRNA, mock transfection, and a cytotoxicity control to separate on‑target effects from delivery toxicity.
• Readouts: RT‑qPCR (ΔΔCt), immunoblot, reporter assays, proteasome activity assays.

These ranges are provided as general literature norms; optimize empirically for your specific cell line and delivery reagent.

Safety and Handling

• GHS classification, Signal word, H‑Statements, Pictograms: Not specified for this item; refer to SDS.
• Intended use: For research use only. Not for human or veterinary use.

General laboratory safety for siRNA/oligonucleotides (literature/practice):

• PPE: Wear lab coat, gloves, and safety glasses. Handle solutions in a clean RNA‑dedicated area to minimize RNase contamination.
• RNase control: Use certified RNase‑free consumables and solutions. Wipe benches and pipettes with RNase decontamination solutions. Change gloves frequently.
• Incompatibilities: Avoid nucleases (RNase A contamination), microbial contamination, and repeated freeze–thaw cycles that may degrade RNA.
• First aid (general): In case of contact with eyes or skin, rinse with water. If inhaled (powder), move to fresh air. If ingested, rinse mouth with water. Seek medical attention if adverse effects occur. Defer to SDS for authoritative guidance.
• Spill response: For small aqueous spills, absorb with disposable towels; decontaminate with RNase‑inactivating solution. Dispose of waste according to institutional biosafety procedures.
• Special risks: Aerosols during transfection setup can spread nucleic acids; work gently and, if needed, in a biosafety cabinet appropriate for your cell line and vector/reagent risk profile.
• Storage risks: Maintain frozen storage to prevent hydrolysis and nuclease activity. Protect from repeated warming and from microbial contamination.

Solvent Selection

As an RNA oligonucleotide reagent, this product is reconstituted and used in aqueous, RNase‑free media rather than organic solvents.

• Primary solvents/buffers (general literature guidance):
  • RNase‑free water (pH ~6.5–8.0)
  • TE buffer (10 mM Tris‑HCl, 0.1–1 mM EDTA, pH 7.5–8.0) to chelate divalent cations and slow RNA hydrolysis
  • Commercial “siRNA buffer” (e.g., 10 mM Tris, 20 mM KCl, 1 mM MgCl2, pH ~7.5) when recommended by transfection reagent providers
• Miscibility: Fully miscible with aqueous cell culture media and transfection mixes. Not compatible with most organic solvents (which precipitate or denature RNA).
• Polarity/dielectric context: Highly polar, polyanionic macromolecules; activity and stability depend on ionic strength and Mg2+/RNase presence.

Selection tips:

• Use RNase‑free water for initial reconstitution and aliquoting; switch to the transfection buffer/media according to your reagent’s protocol.
• For long‑term stock stability, a low‑salt Tris/EDTA buffer at pH 7.5–8.0 is commonly used (literature).
• Avoid phosphate‑rich buffers during some transfections if complexation efficiency with cationic lipids is reduced; follow the transfection reagent’s instructions.

Comparison (general):

• Water: maximal versatility; minimal ionic strength; best for lyophilized reconstitution.
• TE: enhances stability against nuclease/metal‑catalyzed degradation; may slightly reduce complexation with some delivery reagents at high EDTA.
• Culture media: use only after forming complexes with the delivery reagent to maintain complex integrity.

Storage and Reconstitution

Item‑specific storage and shipping:

• Storage conditions: Store at −20 °C (Product Data).
• Shipped in: Ice chest + ice pads (Product Data).
• Research use note: For research use only (Product Data).

Reconstitution (general literature guidance; not item‑specific):

• Upon receipt, briefly centrifuge tubes to collect contents.
• Reconstitute lyophilized material in RNase‑free water or TE buffer to 10–50 µM. Mix gently and allow 10–15 min for complete dissolution.
• Determine concentration by A260 using the extinction coefficient provided on the CoA/Spec Sheet when available.

Aliquoting and storage practice (general):

• Prepare single‑use aliquots to avoid repeated freeze–thaw cycles.
• Store working aliquots at −20 °C as specified. For extended multi‑year storage, many labs use −80 °C (literature); ensure alignment with your QA practices.
• Protect from light only if dye labels are present (not specified for this item).
• Avoid contamination with RNases; use sterile, nuclease‑free tubes and tips.

Stability notes:

• Avoid >3–4 freeze–thaw cycles. Thaw on ice and keep solutions cold during setup.
• If supplied in solution, verify any stabilizers/buffer composition on the CoA; Not specified for this item; refer to CoA/Spec Sheet.

Structure and Identity

This product is a pre-designed small interfering RNA (siRNA) reagent set targeting the human PSMD13 transcript (proteasome 26S subunit, non-ATPase 13). It consists of one or more double‑stranded RNA oligonucleotides intended for sequence‑specific RNAi knockdown in human cells.

• Item type: Pre-designed siRNA Set A against human PSMD13 (gene-level target)
• Molecular formula: Not applicable for heterogeneous oligonucleotide mixtures; Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet. (Typical for a 21‑mer siRNA duplex is ~13–14 kDa, literature.)
• SMILES / InChI / InChIKey: Not applicable to oligonucleotide mixtures.
• Structural features (general, literature):
  • Double‑stranded RNA duplexes with Watson–Crick base pairing; frequently 19‑bp duplex with 2‑nt 3′ overhangs (e.g., dTdT), Dicer‑compatible.
  • Each strand features a 5′ phosphate (or 5′‑OH depending on synthesis and deprotection) and ribose 2′‑OH groups; optional backbone or sugar modifications may be present in some designs (not specified for this item).
  • Antisense (guide) strand complementary to a region of human PSMD13 mRNA; sense (passenger) strand is the corresponding mRNA sequence.
• Gene target: PSMD13 (HGNC: 9534) — non‑ATPase subunit of the 19S regulatory particle of the 26S proteasome (general knowledge).

2D description in words (general): Two short RNA strands annealed to form a duplex helix with 3′ overhangs; the antisense strand is designed to be loaded into RISC for mRNA recognition and cleavage of PSMD13 transcripts.

Synthetic Utility

Not typically applicable. This product is a biological oligonucleotide reagent for RNAi knockdown, not a building block or reagent for chemical synthesis.

For researchers seeking chemical biology adaptations (general literature context):

• siRNA can serve as a functional probe in target validation workflows prior to small‑molecule inhibitor campaigns.
• Sequence information (when provided) can inform design of antisense or CRISPR guide strategies, but the siRNA itself is not used as a synthetic intermediate.

Target Specificity

• Target: Human PSMD13 mRNA (gene symbol: PSMD13), a non‑ATPase subunit of the 19S regulatory particle of the 26S proteasome (general knowledge).
• Species reactivity: Human (intended design target). Cross‑species activity is sequence‑dependent and not guaranteed.
• Set format: Pre‑designed “Set A” typically comprises multiple siRNA duplexes directed to non‑overlapping regions of the target transcript (general literature practice). Exact number, sequences, and target exon positions are Not specified for this item; refer to CoA/Spec Sheet.
• Off‑target considerations (general): Use reduced individual duplex concentration when pooling; confirm phenotype with at least two independent duplexes and rescue experiments when feasible.

Note: Definitive targeting information (individual sequences, predicted off‑targets, and alignment scores) should be obtained from the product’s CoA or design report.

자주 묻는 질문

How should this product be stored?

Store at ?20 °C. Freezer storage is required to maintain the specified shelf life.

How is this product shipped?

This product ships in an insulated container with ice pads. Unpack on arrival and transfer it to the storage condition stated above.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.