TP53BP1 Human Pre-designed siRNA Set A

Cat. No.: T1489652

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Panoramica

TP53BP1 Human Pre-designed siRNA Set A contains three designed siRNAs for TP53BP1 gene (Human), as well as a negative control, a positive control, and a FAM-labeled negative control. Components TP53BP1 siRNA-1: 5 nmol (HPLC) TP53BP1 siRNA-2: 5 nmol (HPLC) TP53BP1 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 applications, validated cell lines, recommended dilutions, and step-by-step procedures are not specified for this item; refer to the product CoA/Spec Sheet and SDS.

For general guidance on use with mammalian cells, see the Reaction Conditions tab in this listing.

Biological Roles

TP53BP1 (Tumor Protein p53 Binding Protein 1) is a key mediator of the DNA damage response (DDR), particularly at DNA double-strand breaks (DSBs).

• Core functions (general biology):
  • Acts as a scaffold at DSBs, recognizing H4K20me2 and H2AK15ub via Tudor/UDR domains to accumulate at damage sites and promote repair complex assembly.
  • Favors non-homologous end joining (NHEJ) by limiting DNA end resection; functionally counterbalances BRCA1 in repair pathway choice.
  • Involved in class-switch recombination and V(D)J recombination in lymphocytes.
  • Participates in checkpoint signaling downstream of ATM and 53BP1 foci formation, integrating chromatin context and cell cycle cues.
• Cellular phenotypes upon reduced TP53BP1 (literature):
  • Diminished 53BP1 ionizing radiation-induced foci (IRIF), altered repair kinetics, increased reliance on homologous recombination in certain contexts, and changes in sensitivity to DSB-inducing agents.
• Research utility of this siRNA set:
  • Enables transient knockdown of human TP53BP1 to dissect DDR mechanisms, test genetic interactions, and benchmark pathway reporters in cultured cells (research use only).

Note: Biological details are provided for context; the magnitude and specificity of knockdown depend on the exact siRNA sequences and cell model. Sequence-level specifications for this item are not provided here.

Buffer Applications

This product is not a buffer component in the classical sense. However, the choice of reconstitution buffer affects stability and performance of siRNA in cell studies.

• Practical reconstitution buffers (general guidance):
  • RNase-free water: Suitable for short-term use; minimizes ionic strength effects during transfection complex formation.
  • TE (10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0): Enhances stability during storage by chelating divalent cations that catalyze RNA hydrolysis.
• pH considerations: Slightly alkaline buffers (pH ~7.5–8.0) are commonly used for long-term stability (literature), but avoid high-pH (>8.5) or low-pH (<6) conditions for prolonged periods.
• Sterility and RNase control: Use certified RNase/DNase-free solutions and consumables; optionally filter sterilize (0.22 µm) before preparing working dilutions.

For electrophoresis or analytical QC, standard native PAGE or denaturing urea-PAGE running buffers apply, but these are method-dependent and not specific to this item.

Green Alternatives

Green chemistry considerations are limited for siRNA use, but sustainable practices can reduce environmental footprint:

• Solvent/buffer choices:
  • Prefer aqueous RNase-free water or TE; avoid single-use nuclease inactivation reagents with hazardous components when not necessary.
• Waste minimization:
  • Consolidate experiments to reduce plastic consumables; use low-retention, recyclable labware where validated.
  • Prepare concentrated stocks (≥20–50 µM) to minimize storage volume and packaging.
• Energy efficiency:
  • Store working aliquots at –20°C rather than ultra-low temperatures when stability permits (per item-specific storage guidance, –20°C is appropriate).
  • Limit freezer door openings; use secondary containment to reduce frost/ice buildup.
• Reagent alternatives:
  • Choose lower-toxicity transfection reagents validated for your cell type; some lipid/polymer systems have improved biocompatibility and lower solvent content (literature-dependent, user-validated).
• Documentation and QC:
  • Use digital records to minimize printing; request electronic CoA and sequences when available to avoid paper waste.

Trade-offs: Some greener transfection reagents may yield slightly lower efficiency, requiring optimization. Reduced plastic usage must be balanced against RNase control and sterility requirements.

Pharmaceutical Uses

No pharmaceutical or clinical use is claimed or supported for this product.

• Status: For research use only (from Product Data). Not intended for diagnostic, therapeutic, or in vivo administration.
• Excipient/formulation role: Not applicable. Any formulation details (e.g., stabilizers, lyoprotectants) are not specified for this item; refer to CoA/Spec Sheet.
• Regulatory: No pharmacopeial monograph or GMP grade is indicated for this catalog product.

If translational studies are contemplated, separate sourcing under appropriate regulatory frameworks and quality systems would be required; this product is not designated for such use.

Physical Properties

Item-specific physical data

• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
• Appearance: Not specified for this item; refer to CoA/Spec Sheet (commonly supplied lyophilized or in RNase-free solution).
• BP/MP, density, refractive index, logP: Not applicable for oligonucleotides; not specified for this item.

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

• State: Typically supplied lyophilized or in aqueous buffer; forms clear solutions in RNase-free water or TE buffer (10 mM Tris, 0.1–1 mM EDTA, pH 7.5–8.0).
• Solubility: Highly soluble in water; insoluble in most organic solvents.
• pKa: Multiple ionizable phosphate groups render siRNA polyanionic at physiological pH.
• UV absorption: Strong at 260 nm; sequence-dependent molar extinction coefficient (ε260) is calculable but sequence-specific and thus not provided for this item.
• Thermal behavior: Duplex melting temperature (Tm) depends on length, GC content, and salt concentration; typically in the 50–80°C range for 19–21-mers (literature, sequence-dependent).
• Stability: Enhanced at –20°C or below, protected from moisture and RNases; repeated freeze–thaw can degrade RNA.

Practical notes

• Reconstitution is commonly performed to 10–100 µM in RNase-free water or TE; vortexing is avoided to minimize shearing; gentle pipetting recommended.
• For accurate quantification, A260 can be used after reconstitution, but sequence-specific ε is required (not provided here).

Quality and Grades

Item-specific quality details

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

What a pre-designed siRNA set typically implies (general/literature context)

• Set composition: Multiple distinct siRNA duplexes targeting different regions of the human TP53BP1 transcript to mitigate sequence-specific off-target effects and enable selection of the most effective duplex in a given cell line.
• Typical QC (general, not item-specific): Identity confirmation by MALDI-TOF MS or ESI-MS; purity by HPLC or PAGE; residual salts/solvents testing; endotoxin testing for cell-based applications. Exact specifications for this product are not provided here.
• Performance expectations: Effective knockdown windows often 24–96 h post-transfection; efficiency depends on cell type, delivery reagent, and duplex sequence.
• Documentation: For sequence, modification pattern, amount (nmol/OD260), and analytical traces, consult the product’s CoA/Spec Sheet.

Research-only status

• Labeled for Research Use Only. Not intended for diagnostic, therapeutic, or in vivo use without appropriate approvals and validation.

Reaction and Applications

As a functional genomics tool, this siRNA set is used to mediate RNA interference (RNAi) and transiently suppress expression of human TP53BP1 in cultured cells for mechanistic studies.

• Core application areas (general/literature):
  • DNA damage response mapping: TP53BP1 knockdown to probe non-homologous end-joining (NHEJ) vs homologous recombination balance, 53BP1 foci kinetics after IR/DSB-inducing agents.
  • Pathway epistasis: Combine with siRNA/CRISPR perturbations of BRCA1, RIF1, REV7, or Shieldin components to examine repair pathway choice.
  • Synthetic interaction studies: Assess sensitivity to PARP inhibitors or replication stressors in the context of reduced TP53BP1 levels (research use only).
  • Proteomics/transcriptomics: RNA-seq or IP-MS after knockdown to delineate downstream transcriptional and interactome changes.
• Practical tips (general):
  • Use multiple duplexes from the set; select the top-performing one(s) based on mRNA knockdown by qRT-PCR and protein reduction by Western blot or immunofluorescence.
  • Include controls: non-targeting siRNA, positive knockdown control, and mock-transfection.
  • Optimize transfection reagent, siRNA dose (1–50 nM), and cell density; maintain consistent serum conditions.
  • Confirm on-target activity by rescue with siRNA-resistant cDNA where feasible.
• Readouts: γH2AX/53BP1 foci imaging, comet assays, reporter-based NHEJ/HR assays (e.g., EJ5-GFP, DR-GFP) to functionally verify phenotypes following TP53BP1 suppression.

Reaction Conditions

No chemical reaction conditions apply. The relevant “conditions” concern transfection and cellular knockdown (general literature guidance; optimize empirically):

• Cell density at transfection: 40–70% confluence for adherent lines; aim for logarithmic growth.
• siRNA working concentration: 1–50 nM; start with 5–10 nM and titrate.
• Complexation: Mix siRNA with a compatible transfection reagent (lipid or polymer) in serum-free medium for 5–20 min to allow complex formation; then add to cells. Some reagents support direct complexation in complete medium—follow reagent instructions.
• Medium: Many protocols tolerate 10% FBS; serum-free exposure during the first 2–6 h can improve uptake with certain reagents.
• Incubation: Replace medium after 4–24 h if cytotoxicity is observed; otherwise maintain until harvest.
• Knockdown window: Assess mRNA reduction at 24–48 h, protein depletion at 48–96 h; longevity depends on target protein turnover.
• Controls: Non-targeting siRNA, positive knockdown control, and mock complexes. Include toxicity controls for the transfection reagent.
• Readouts: qRT-PCR, Western blot, immunofluorescence foci (53BP1/γH2AX), and functional DSB repair reporters.

All parameters are general recommendations from the literature; follow cell line– and reagent-specific protocols. Item-specific validated conditions are not provided here.

Safety and Handling

Item-specific safety information

• GHS classification, pictograms, signal word, H-statements: Not specified for this item; refer to the SDS.
• Research Use: For research use only (from Product Data).

General safe-handling guidance for siRNA (not item-specific; defer to SDS for authoritative details)

• PPE: Laboratory coat, gloves (nitrile), safety glasses. Use RNase-free practices to prevent degradation (dedicated RNase-free tips/tubes, cleaned benches, avoid touching tube rims).
• Avoid inhalation of powders/aerosols; handle lyophilized material in a clean area. Prevent exposure to RNases from skin; change gloves frequently.
• Incompatibilities: Strong nucleases (RNases), extreme pH (<6 or >9) for prolonged periods, and multiple freeze–thaw cycles can degrade RNA. Avoid microbial contamination.
• First aid (general): If inhaled—move to fresh air. Skin contact—wash with soap and water. Eye contact—rinse cautiously with water for several minutes. Ingestion—rinse mouth; seek medical advice. Provide SDS to medical personnel.
• Spill/cleanup: Collect solids with disposable spatula and wet-wipe surfaces using RNase decontamination solution; dispose of waste per institutional and local regulations.
• Fire: Product is aqueous/biopolymer and not highly flammable; use appropriate extinguishing media for surrounding materials.
• Transport: Shipments commonly with cold packs; maintain cold chain on receipt, minimizing time at ambient temperature.

Solvent Selection

This product is a nucleic-acid reagent, not a small-molecule solute; classical organic solvent selection is not applicable. The relevant consideration is reconstitution/dilution medium for cell-based delivery.

• Primary choices (general guidance):
  • RNase-free water: Maximizes simplicity and reduces ionic strength; suitable for short-term storage and immediate use.
  • TE buffer (10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0): Helps chelate divalent cations that catalyze RNA hydrolysis; improves long-term stability, especially for stock solutions.
• Avoid: Biological media for long-term storage (risk of nucleases), extreme pH buffers, or any solution suspected of RNase contamination. Do not dissolve in organic solvents.
• Concentration selection: Common stock concentrations are 10–100 µM; working concentrations in cells are typically 1–50 nM (literature; optimize per cell line and transfection method).
• Filtration: If sterility is required, use 0.22 µm low-binding filters; minimize shear and adsorption losses.
• Adsorption mitigation: Use low-retention tubes/tips; include carrier (e.g., 0.1 mM EDTA) if ultra-dilute.

Storage and Reconstitution

Item-specific storage and shipping (from Product Data)

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

General/literature guidance (not item-specific; verify with CoA)

• Upon receipt: If lyophilized, briefly centrifuge before opening to collect material. Equilibrate to room temperature in a desiccator before opening to minimize moisture uptake.
• Reconstitution: Use RNase-free water or TE buffer (10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0) to prepare stocks at 10–100 µM. Mix gently; avoid vigorous vortexing.
• Aliquoting: Divide into single-use aliquots to avoid repeated freeze–thaw. Use low-retention tubes.
• Storage of solutions: Store at –20°C (short-to-mid term) protected from light; for extended storage, –80°C is commonly used in the literature. Avoid >3–4 freeze–thaw cycles.
• Thawing: Thaw on ice, mix gently, quick-spin, and keep cold during setup. Keep working dilutions on ice and discard leftovers to limit RNase exposure.
• Stability: Long-term stability is sequence- and formulation-dependent; exact shelf life and acceptable freeze–thaw cycles are not specified for this item and should be confirmed on the CoA/Spec Sheet.

Always maintain RNase-free conditions during handling and storage.

Structure and Identity

Item-specific facts (from Product Data)

• Product: TP53BP1 Human Pre-designed siRNA Set A (SKU: T1489652)
• Type: Pre-designed small interfering RNA (siRNA) duplex set targeting human TP53BP1 mRNA
• CAS/CID/InChIKey/SMILES: Not applicable to siRNA and not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula and molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

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

• siRNA typically consists of a short double-stranded RNA with phosphodiester backbone, about 19–21 base pairs with 2-nt 3′ overhangs (often dTdT).
• Each duplex comprises an antisense (guide) strand complementary to target mRNA and a sense (passenger) strand.
• Key structural motifs enabling function include a 5′-phosphate on the guide strand for RISC loading and A-form helical geometry characteristic of dsRNA.
• Optional chemical stabilizations (e.g., 2′-O-Me, 2′-F ribose, phosphorothioate linkages) are commonly used in the field, but the presence/absence of modifications for this specific product is not specified; refer to CoA/Spec Sheet.

2D structural features in words (general)

• Linear polymers of ribonucleotides linked by 3′→5′ phosphodiester bonds, forming two antiparallel strands with Watson–Crick base pairing (A•U and G•C) and short single-stranded overhangs at the 3′ ends.

Synthetic Utility

As a biologic oligonucleotide reagent, this product is not a classical synthetic building block. Its “synthetic utility” resides in chemical biology and functional genomics workflows:

• Targeted gene silencing (general): Programmable suppression of TP53BP1 expression enables construction of defined cellular states to probe DNA repair pathways, checkpoint control, and chromatin signaling.
• Perturbation–response mapping: Integrate with small-molecule modulators (e.g., DDR inhibitors) to generate combination perturbations and map causal networks.
• Screening and validation: Use across cell line panels to evaluate context-specific dependencies; select the most potent duplex from the set to carry forward into mechanistic assays.
• Rescue and domain-mapping studies: Combine knockdown with expression of siRNA-resistant TP53BP1 variants to dissect domain contributions (e.g., Tudor vs. BRCT) to observed phenotypes.
• Multi-omic integration: Pair RNAi with transcriptomics, proteomics, and imaging to link TP53BP1 depletion to pathway-level changes.

Note: Chemical transformations or stoichiometric organic reactions are not applicable to this reagent.

Target Specificity

Item-specific details

• Intended target: Human TP53BP1 mRNA (Tumor Protein p53 Binding Protein 1).
• Set design: Pre-designed siRNA duplex set (“Set A”). Number of duplexes, sequences, and target regions: Not specified for this item; refer to CoA/Spec Sheet.

General considerations (literature; not item-specific)

• Pre-designed sets usually include multiple non-overlapping guides to reduce the risk of sequence-specific off-targets and to identify the most effective duplex in a given cell type.
• Off-target mitigation strategies include using the lowest effective concentration, seed-region analysis, and confirmatory phenotyping with ≥2 independent siRNAs.

No additional antigen/epitope/clone details apply, as this is not an antibody product.