Dnajb1 Mouse Pre-designed siRNA Set A

Cat. No.: D1487391

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Panoramica

Dnajb1 Mouse Pre-designed siRNA Set A contains three designed siRNAs for Dnajb1 gene (Mouse), as well as a negative control, a positive control, and a FAM-labeled negative control. Components Dnajb1 siRNA-1: 5 nmol (HPLC) Dnajb1 siRNA-2: 5 nmol (HPLC) Dnajb1 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.

Application Protocols

Tested/validated application protocols, recommended dilutions, and positive controls for this specific item are not provided in the Product Data.

• Item-specific usage instructions: Not specified for this item; refer to CoA/Spec Sheet and SDS.

Note: General transfection guidance is provided in the Reaction Conditions section as literature-based, non-item-specific best practices.

Biological Roles

Target context (literature)

• Dnajb1 encodes a member of the Hsp40/DNAJ family (co-chaperones for Hsp70). DNJB1 proteins stimulate Hsp70 ATPase activity, facilitating protein folding, maturation, and proteostasis.
• Functions attributed to Hsp40/DNAJ family members include client protein delivery to Hsp70, prevention of aggregation, assistance in refolding or targeting misfolded proteins for degradation, and participation in stress responses (heat shock, oxidative stress).
• Subcellular localization: predominantly cytosolic with potential association to various client protein complexes (species- and isoform-specific; literature).

Relevance of gene knockdown (research use, literature)

• Reducing Dnajb1 expression enables interrogation of chaperone-dependent pathways, proteostasis networks, and stress-response signaling in mouse cell models.
• Phenotypic readouts may include alterations in client protein stability, unfolded protein response markers, or sensitivity to proteotoxic stressors.

Caveats

• Gene family redundancy: other DNAJ/Hsp40 members may compensate; consider parallel or pooled knockdowns for pathway mapping.
• Off-target considerations: use multiple independent siRNA duplexes (as provided in a set) and perform rescue experiments to confirm specificity.

Item-specific biological details

• Specific transcript isoforms targeted, exon locations, and sequence data: Not specified for this item; refer to CoA/Spec Sheet.

Buffer Applications

Applicability

• siRNA reagents are not buffer components per se; however, buffer choice critically influences siRNA stability and transfection performance.

General/literature guidance

• Reconstitution: RNase-free water or TE (10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0). TE provides improved long-term stability by chelating divalent cations that promote RNA hydrolysis.
• Working solutions: Prepare immediately before use in cell-culture compatible media (e.g., serum-free Opti-MEM) for complex formation with transfection reagents. After complexing, add to complete growth medium as per reagent instructions.
• pH considerations: Maintain near-neutral pH (7.0–8.0). Avoid strong alkaline conditions that accelerate RNA backbone cleavage.
• Ionic strength: High salt can affect complexation with cationic lipids/polymers; follow reagent-specific recommendations, typically using reduced-serum or serum-free media during complex formation.
• RNase control: Use certified RNase/DNase-free consumables; treat surfaces with RNase decontamination solutions.

Item-specific buffer recommendations

• Not specified for this item; refer to CoA/Spec Sheet for any recommended reconstitution buffer or concentration.

Green Alternatives

Context

• siRNA-based gene silencing typically involves aqueous solutions and microliter-scale reagents, with a comparatively small solvent footprint relative to many organic syntheses. Nevertheless, greener practices can further reduce environmental impact.

Greener choices and trade-offs (literature/general)

• Buffer selection: use minimal volumes of RNase-free water or TE; avoid single-use plastic by planning aliquots efficiently. Trade-off: more aliquots can increase plastic use—balance by right-sizing aliquots.
• Transfection reagents: newer lipid formulations can reduce required reagent mass and cytotoxicity; select reagents that perform at low doses in your cell line to minimize waste. Trade-off: screening may be required.
• Waste management: segregate non-hazardous aqueous oligo waste from hazardous organic waste streams; neutralize and dispose per local regulations.
• Energy use: store working stocks at −20°C rather than −80°C when stability permits (siRNA is generally stable at −20°C), reducing energy consumption.

Brief comparison table (general)

• RNase-free water vs TE buffer: water has lower chemical footprint but may shorten solution shelf-life; TE prolongs stability but adds chelator components.

Item-specific environmental notes

• Not specified for this item; consult institutional sustainability guidelines for oligonucleotide workflows.

Pharmaceutical Uses

This product is designated For research use only and is not intended for human or veterinary use, diagnostics, or as a drug substance/excipient.

General context (literature)

• siRNA oligonucleotides can serve as active pharmaceutical ingredients in regulated settings when manufactured under GMP with defined sequences, purity, and delivery systems. Such uses require extensive characterization, stabilization chemistries, and validated formulations. None of these claims or qualifications apply to this catalog research item unless explicitly stated in its documentation.

Formulation-related notes for research settings

• For in vitro research, siRNA is typically formulated transiently with transfection reagents and not as a stable pharmaceutical dosage form.
• For in vivo research, specialized carriers (lipid nanoparticles, conjugates) are often required; suitability, modifications, and sterility for such applications are not specified for this item and must be evaluated independently.

Item-specific pharmacopeial/GMP status

• Not specified for this item; refer to CoA/Spec Sheet. No GMP or pharmacopeial compliance is stated in the provided data.

Physical Properties

Item-specific specifications

• Molecular weight, extinction coefficient, concentration, and sequence-specific properties: Not specified for this item; refer to CoA/Spec Sheet.

General/literature properties for siRNA oligonucleotides

• Physical state: typically supplied lyophilized or in aqueous buffer; forms clear colorless solutions when reconstituted in RNase-free water or TE (literature).
• Solubility: highly soluble in RNase-free water and low-salt buffers; limited solubility in organic solvents (literature).
• UV absorbance: strong absorbance at 260 nm; A260 can be used to estimate concentration using sequence-dependent extinction coefficients (literature). If no sequence is provided, mass-based reconstitution is preferred.
• pKa/logP: Not meaningful for polyanionic biopolymers; macroscopic pKa dominated by phosphate groups (literature).
• Melting temperature (Tm): duplex Tm depends on length, GC content, salt, and modifications; 19–23-mers typically melt between ~55–85°C in physiological ionic strength (literature). Specific Tm values for this set: Not specified for this item; refer to CoA/Spec Sheet.
• Stability: dry, protected from moisture at ≤−20°C for extended periods; in solution, more stable at −20°C in RNase-free, low-salt buffers; avoid repeated freeze–thaw (literature).
• Compatibility: stable across pH ~6.5–8.5; degraded by RNases and under strong alkaline conditions (literature).

Note: Do not treat literature values as specifications; consult the item’s CoA/Spec Sheet for any guaranteed properties.

Quality and Grades

Item-specific quality information

• Grade/purity and specific QC metrics: Not specified for this item; refer to CoA/Spec Sheet.

General guidance on siRNA quality (literature/industry practice)

• Typical QC for research-grade siRNA includes OD260 quantitation, mass confirmation by MS, and purity assessment by PAGE or HPLC. Common specifications are reported as percentage full-length product and residual salts/solvents; exact values vary by supplier and product line.
• Pre-designed siRNA sets commonly include multiple non-overlapping duplexes targeting a single gene to maximize knockdown success and to enable pooled use for potency and reduced off-target effects.
• Stabilizers/modifications: Some siRNAs incorporate 2′-O-Me/2′-F and/or phosphorothioate linkages at select positions to enhance nuclease resistance and reduce innate immune activation; whether this set includes such modifications is Not specified for this item; refer to CoA/Spec Sheet.
• Research vs. GMP: Unless explicitly stated, pre-designed siRNAs are intended for research use only and are not manufactured under GMP. This item carries the note: For research use only (from Product Data).

Implications for end users

• For quantitative work, rely on the supplied CoA for mass, purity, and any extinction coefficient. If sequence is undisclosed, use mass-based reconstitution rather than A260 unless the CoA provides the necessary constants.
• If comparing across lots, request the same synthesis scale and purification grade to minimize variability.

Reaction and Applications

Scope of use (research-only)

• This pre-designed siRNA set targets mouse Dnajb1 to enable transient gene knockdown at the mRNA level in mammalian cells for pathway interrogation, target validation, and phenotype studies.

Mechanistic background (literature)

• siRNA duplexes are incorporated into the RNA-induced silencing complex (RISC). The passenger strand is removed, while the guide strand directs Argonaute to complementary Dnajb1 mRNA, promoting endonucleolytic cleavage and/or translational repression.

Typical applications (literature)

• In vitro cell-based knockdown: transfect adherent or suspension mouse cell lines using cationic lipids or polymers; assess mRNA by RT-qPCR and protein by immunoblotting 24–72 h post-transfection.
• Pooled siRNA use: combining multiple duplexes from the set can enhance potency and mitigate off-targets by reducing the effective concentration of each guide while maintaining on-target activity.
• Rescue experiments: co-express siRNA-resistant DNJB1 constructs (e.g., with silent mutations) to verify on-target phenotypes.

Practical tips (literature)

• Optimize siRNA dose (commonly 5–50 nM final) and transfection reagent ratio per cell type.
• Include non-targeting and positive-control knockdown siRNAs to benchmark performance.
• Validate knockdown at both RNA and protein levels; stagger timepoints to capture primary vs. secondary effects.

Item-specific application notes

• Manufacturer Applications provided: none beyond title; no additional validated uses are specified for this item.

Reaction Conditions

Scope

• There are no chemical reactions in the conventional sense; conditions refer to transfection and gene-silencing workflows.

General/literature guidance for siRNA transfection

• Cell density: seed cells to reach 50–70% confluence at transfection time for adherent lines; optimize for your model.
• Dose: start with 5–10 nM siRNA final; titrate up to 50 nM if needed while monitoring cytotoxicity and off-target effects.
• Complexation: dilute siRNA and transfection reagent separately in serum-free medium (e.g., Opti-MEM); combine and incubate 10–20 min at room temperature to form complexes (follow reagent IFU).
• Incubation: replace with complete medium after 4–24 h depending on reagent; analyze mRNA at 24–48 h and protein at 48–96 h.
• Controls: include non-targeting siRNA, positive-control knockdown, and mock transfection. Perform dose–response and time-course experiments.
• Readouts: RT-qPCR for Dnajb1 mRNA; immunoblotting/ELISA for DNJB1 protein; functional phenotypes under proteotoxic stress.

Tips to maximize performance (literature)

• Use RNase-free technique; prepare single-use aliquots to avoid freeze–thaw.
• Minimize serum during complexation if required; some reagents are serum-tolerant—verify with the manufacturer’s IFU.
• Pooling: combine equimolar amounts of duplexes from the set to a total of 5–20 nM for robust knockdown while reducing off-target risk.

Item-specific tested conditions

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

Safety and Handling

GHS/Classification (item-specific)

• Signal word, H-statements, pictograms, and GHS classification: Not specified for this item; refer to the product SDS for authoritative safety information.

General safe handling practices for siRNA reagents (literature/standard lab practice)

• Expected hazards: siRNAs are non-volatile, non-flammable aqueous/solid biopolymers; primary risk is irritation/allergy upon contact or inhalation of powders/aerosols. Handle to avoid aerosolization.
• PPE: laboratory coat, nitrile gloves, and safety glasses. Use RNase-free, dedicated tools and barrier tips to prevent contamination. Change gloves frequently to prevent RNase transfer.
• Engineering controls: work in a clean area; for sterile/aseptic prep, use a biosafety cabinet. Avoid open handling if generating aerosols.
• Incompatibilities: nucleases (RNases) rapidly degrade siRNA. Avoid contact with biological samples or surfaces contaminated with RNase; clean benches and tools with RNase decontamination solutions. Avoid strong bases/acids and oxidizers that may hydrolyze RNA.
• First aid (overview): skin/eye contact—rinse with water; inhalation—move to fresh air; ingestion—rinse mouth. Seek medical attention as needed. Provide SDS to responders.
• Spills: avoid dust; gently collect solids; for solutions, absorb with inert material. Decontaminate with RNase-inactivating solutions if needed.
• Waste: dispose of according to institutional policies for non-hazardous laboratory biological chemicals; if mixed with transfection agents or hazardous buffers, follow appropriate waste streams.

Always consult the SDS and institutional EHS guidance before use.

Solvent Selection

Applicability

• siRNA duplexes are hydrophilic polyanions; dissolution is performed in aqueous, RNase-free media. Organic solvent selection is generally not applicable.

Recommended solvents/buffers (literature)

• RNase-free water (nuclease-free): default solvent for initial dissolution.
• TE buffer (10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0): improves stability by chelating divalent cations that catalyze RNA degradation.
• PBS or Opti-MEM (for transfection complexation): prepare working dilutions immediately before use; avoid long-term storage in salt-rich buffers.

Practical notes

• Warm to room temperature before opening to avoid condensation; briefly spin down lyophilized material before opening.
• Avoid repeated freeze–thaw; prepare single-use aliquots in RNase-free tubes.
• Avoid solutions with bivalent cations (Mg2+, Ca2+) during storage as they can promote nuclease activity; include EDTA if compatible with downstream use.

Comparison (general)

• RNase-free water: maximal compatibility, but slightly less stability over long-term than TE.
• TE buffer: increased long-term stability; ensure EDTA does not interfere with downstream enzymatic steps or cell culture transfection conditions.

Item-specific solvent guidance

• Not specified for this item; refer to CoA/Spec Sheet for any provided reconstitution buffer or concentration recommendations.

Storage and Reconstitution

Item-specific instructions (from Product Data)

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

General/literature guidance

• Upon receipt: If lyophilized, centrifuge briefly before opening to collect material. Allow to warm in a desiccator or at room temperature before opening to prevent condensation.
• Reconstitution solvent: RNase-free water or TE buffer (10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0). If no extinction coefficient is supplied, reconstitute to a convenient molar concentration by mass (e.g., 10–50 µM) and record aliquot volumes.
• Aliquoting: Prepare single-use aliquots to avoid repeated freeze–thaw cycles. Use RNase-free, low-bind tubes. Label with concentration and date.
• Storage of solutions: Store at −20°C (preferred) or 2–8°C for short-term (≤1 week). Avoid >3 freeze–thaw cycles. Protect from nucleases and microbial contamination.
• Thawing/handling: Thaw on ice, mix gently (do not vortex vigorously), and briefly spin down before use. Keep on ice during setup.
• Stability: Dry siRNA is generally stable for many months at −20°C; solutions are stable for weeks to months at −20°C depending on buffer and sterility (literature). Exact shelf-life for this item: Not specified for this item; refer to CoA/Spec Sheet.

Compatibility notes

• Avoid prolonged storage in high-salt buffers or with divalent cations. Ensure any EDTA present in TE does not interfere with downstream applications.

Structure and Identity

Item-specific facts (from Product Data)

• Product type: Pre-designed siRNA duplex set targeting mouse Dnajb1 (Heat shock protein family Hsp40 member B1)
• SKU: D1487391
• CAS, CID, InChIKey, SMILES: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula and exact molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

General/literature description of structure (for siRNA reagents)

• siRNA are typically short, double-stranded RNA duplexes of ~19–23 base pairs with 2-nt 3′ overhangs (commonly UU or dTdT) (literature).
• Each duplex comprises an antisense (guide) strand that is complementary to the target mRNA and a sense (passenger) strand (literature).
• Backbone: ribose-phosphate with 2′-hydroxyl groups; some commercial siRNAs may include optional chemical stabilizations (e.g., 2′-O-Me, 2′-F, phosphorothioates) at select positions to enhance stability and reduce off-targets (literature). Specific modifications for this item: Not specified for this item; refer to CoA/Spec Sheet.
• Structural features relevant to function: 5′-phosphate (or phosphorylatable) ends enable RISC loading; thermodynamic asymmetry across the duplex favors guide-strand selection (literature).

2D structural description in words (literature)

• Two antiparallel RNA strands aligned in A-form helical geometry with periodic minor/major grooves; ~2 nt 3′ overhangs on both strands; free 5′ termini available for RISC interaction; base-pairing via Watson–Crick G≡C and A=U pairs with occasional wobble G•U depending on design. Sequence details for this specific set: Not specified for this item; refer to CoA/Spec Sheet.

Synthetic Utility

Not a chemical building block or reagent

• This product is a biological oligonucleotide reagent (siRNA set) and is not typically used as a substrate, catalyst, or solvent in synthetic organic chemistry.

Relevant utility in experimental design (literature)

• Functional genomics tool: used to perturb gene expression transiently, enabling structure–function studies, pathway mapping, and target validation.
• Mechanistic dissection: knockdown of Dnajb1 can reveal client dependencies on Hsp70/DNAJ chaperone systems and proteostasis mechanisms.

If your goal is chemical synthesis rather than gene modulation

• See other catalog sections for small-molecule building blocks, catalysts, and solvents. For cellular assays, integrate this siRNA with appropriate small-molecule chaperone modulators to build chemical-biology workflows.

Item-specific synthetic roles

• Not applicable.

Target Specificity

Item-specific data required for this section (e.g., individual siRNA sequences, target exon positions, specificity analyses, off-target screening results, and species reactivity) are not provided in the Product Data.

• Target gene: Mouse Dnajb1 (by product name only).
• Sequence(s), alignment details, and off-target analyses: Not specified for this item; refer to CoA/Spec Sheet.
• Validated cross-species reactivity or isoform selectivity: Not specified for this item; refer to CoA/Spec Sheet.