BRD4 Human Pre-designed siRNA Set A

Cat. No.: B1460057

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

BRD4 Human Pre-designed siRNA Set A contains three designed siRNAs for BRD4 gene (Human), as well as a negative control, a positive control, and a FAM-labeled negative control. Components BRD4 siRNA-1: 5 nmol (HPLC) BRD4 siRNA-2: 5 nmol (HPLC) BRD4 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

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

This product requires cold chain shipping. Ground and other economy services are not available.

Product Line

Biological Products

Application Protocols

Only product‑specific, tested protocols and conditions may be listed here. These are not provided in the product data.

• Recommended applications, dilution ranges, complexation parameters, and positive controls: Not specified for this item; refer to the product data sheet/CoA and your transfection reagent manufacturer’s protocol.

Note: While general siRNA transfection workflows are widely available, follow item‑specific instructions when provided to ensure optimal performance.

Biological Roles

General biology of the target (BRD4) and siRNA mechanism (literature):

• BRD4 function: a member of the BET (bromodomain and extra‑terminal) family, BRD4 contains two N‑terminal bromodomains (BD1, BD2) that recognize acetyl‑lysine marks on histones and non‑histone proteins, and an extraterminal domain that recruits transcriptional machinery. BRD4 acts as a chromatin reader linking enhancer/promoter acetylation to productive transcriptional elongation, in part through interactions with P‑TEFb (CDK9/Cyclin T) and Mediator.
• Isoforms: major long (isoform A) and short (isoform C) variants with distinct C‑termini; they can have differential roles in enhancer residence time and gene regulation (literature/general).
• Cellular processes: BRD4 influences cell cycle progression, DNA damage responses, super‑enhancer maintenance, and inflammatory gene expression programs. It can stabilize pause‑release of RNA Pol II and coordinate enhancer‑promoter loops.
• siRNA mechanism: exogenous duplex siRNA is incorporated into RISC; the guide (antisense) strand directs Ago2 to complementary BRD4 mRNA, producing endonucleolytic cleavage and decay, reducing protein levels. Knockdown kinetics are transient, with mRNA reduction evident within 24–48 hours and protein nadirs often at 48–72 hours depending on turnover (literature).
• Controls and specificity: use non‑targeting controls and rescue with siRNA‑resistant BRD4 constructs to confirm on‑target effects. Seed‑based off‑targets can be mitigated by pooling multiple siRNAs at lower individual concentrations.

This information is provided for research context only.

Buffer Applications

As an siRNA reagent, this product is not used as a classical buffer component. However, buffer choice is critical for stability and performance of siRNA in research workflows (general guidance):

• Stock preparation:
  • RNase‑free water (pH ~7) is suitable for initial resuspension. For longer‑term stability, 1× TE (10 mM Tris‑HCl, 1 mM EDTA, pH 7.5–8.0) helps chelate divalent cations that catalyze RNA hydrolysis.
  • Avoid phosphate buffers containing Mg2+/Ca2+ unless needed for a specific protocol; divalent cations can accelerate backbone cleavage.
• Working dilutions for transfection: prepare in serum‑free, RNase‑free medium (e.g., Opti‑MEM) immediately before complexation with delivery reagents; add complexes to complete growth medium after the vendor‑recommended incubation.
• pH range: most siRNA is stable near neutral pH; acidic or strongly basic conditions increase depurination or 2′‑OH–mediated transesterification (literature).
• Ionic strength: moderate monovalent salt (50–150 mM Na+) supports duplex stability; very low ionic strength may reduce Tm, while very high salt can influence complexation behavior.
• Storage buffers: small aliquots in water or TE at −20 °C minimize freeze–thaw. Inclusion of EDTA is generally beneficial for long‑term storage when metal contamination is a risk.

Item-specific buffer recommendations are not specified; follow the CoA/Spec Sheet when provided.

Green Alternatives

Green chemistry considerations for siRNA studies focus on minimizing hazardous auxiliary materials rather than changing the nucleic acid itself.

Opportunities and tradeoffs (general/literature):

• Transfection reagents:
  • Greener choice: biodegradable, serum‑compatible lipid formulations or polymeric systems with reduced cytotoxicity and improved aqueous handling.
  • Tradeoff: may require higher doses or longer incubation to match knockdown efficiencies of legacy cationic lipids.
• Process solvents:
  • Greener choice: eliminate alcohol or DMSO carriers; prepare siRNA stocks in RNase‑free water or TE. Avoid chloroform‑based lipid handling when possible.
  • Tradeoff: some lipoplex formulations historically used organic cosolvents; ensure compatibility with your delivery reagent when switching.
• Plastic waste reduction:
  • Greener choice: plan batching to minimize consumables, use low‑waste 96‑well formats, and adopt RNase‑decontamination solutions with lower environmental impact.
  • Tradeoff: miniaturization can increase evaporation; careful sealing and humidity control are needed.
• Energy use:
  • Greener choice: consolidate freeze–thaw cycles by aliquoting; use -20 °C rather than -80 °C if validated by the vendor (this item specifies -20 °C storage). Shipments already use ice pads; avoid dry ice where not required.

Comparison snapshot (general):

• Conventional approach: siRNA in RNase‑free water + legacy cationic lipid; possible solvent pre‑dilutions and higher cell stress.
• Greener approach: siRNA in water/TE + modern biodegradable lipid; reduced hazardous solvent use and improved cell viability with equal or better silencing after optimization.

Pharmaceutical Uses

This product is for research use only. No medical, diagnostic, or therapeutic use is intended or permitted.

General context (non‑clinical, formulation science perspective):

• siRNAs are widely studied as active oligonucleotide agents in investigational settings. However, pre‑designed research siRNAs, such as a BRD4 siRNA set, are intended for in vitro or exploratory in vivo research and are not produced under GMP nor aligned with pharmacopeial monographs unless specifically stated (not specified for this item).
• Excipient interactions: in formulation research, siRNA physicochemical behavior is influenced by ionic strength, pH, and complexation with delivery systems (lipid nanoparticles, polymers). These considerations may inform preformulation screening, but are outside the scope of this catalog item’s intended use.
• Regulatory status: not a drug substance or excipient; no compendial status claimed or implied for this item.

If translation to preclinical formulation studies is envisioned, separate procurement of GMP‑like or GLP‑grade material, full sequence disclosure, impurity profiling, and stability studies under ICH guidelines would be required. Those attributes are not specified for this research‑grade listing.

Physical Properties

Item-specific physical property data are not provided; refer to CoA/Spec Sheet for exact values.

General/literature properties of siRNA duplexes:

• Physical state: typically supplied lyophilized or in aqueous buffer; appears as a white to off‑white solid or clear/colorless solution at working concentrations.
• Solubility: highly soluble in RNase‑free water and low‑ionic-strength buffers; insoluble in most organic solvents (literature/general).
• pKa/logP: not applicable in the conventional small‑molecule sense due to polyanionic, macromolecular nature; strong negative charge from phosphate backbone dominates behavior (literature/general).
• Density/BP/MP: not meaningful or routinely reported for oligonucleotides; thermal transitions are described by melting temperature (Tm) rather than MP. Duplex Tm depends on sequence, length, salt, and modifications; typical 21‑mer siRNA Tm often >60 °C in 100 mM monovalent salt (literature/general); item‑specific Tm not specified.
• UV characteristics: typical RNA ε260 ≈ 10,000–12,000 M−1·cm−1 per nucleotide (literature/general). Precise extinction coefficients depend on sequence and are not specified for this item.
• Stability: duplex integrity is sensitive to RNases and elevated temperature; stabilizing modifications and low‑temperature storage improve shelf life (literature/general). Exact stability data for this item are not specified.

Refractive index, dielectric constant, and other small‑molecule descriptors are not applicable to siRNA and are not specified for this item.

Quality & Grades

Item-specific grade/purity and stabilizer information are not specified for this item; refer to CoA/Spec Sheet.

General notes on quality for pre‑designed siRNA sets (literature/practice):

• Design rationale: sets typically include 2–4 siRNA duplexes per gene to mitigate off‑target effects and provide redundancy. Each duplex is bioinformatically screened for target specificity, thermodynamic asymmetry (to favor antisense strand loading), and minimized seed-based off‑targets.
• Manufacturing quality: high‑quality siRNAs are synthesized via solid‑phase phosphoramidite chemistry with rigorous deprotection, desalting, and often HPLC or PAGE purification. QC may include MALDI‑TOF or ESI‑MS mass confirmation, UV concentration assay, endotoxin testing for cell work, and absence of residual salts/solvents. For this item, specific purification level and QC tests are not specified.
• Stabilizers/modifications: chemical modifications (e.g., 2′‑O‑Me, 2′‑F, PS linkages) can improve nuclease resistance and reduce innate immune activation; presence/extent not specified for this item.
• Documentation: for reproducibility and regulatory record‑keeping in research, request and retain the item’s sequence list, individual duplex IDs, lot‑specific CoA, and any provided design scores. These documents enable cross‑study comparisons and troubleshooting.
• Performance assurance: in practice, vendors validate silencing efficiency in representative cell lines by qPCR and/or western blot; item‑specific validation data are not provided here.

Reaction & Applications

Manufacturer Applications: Not specified in the product data.

General research applications for BRD4‑targeting siRNA (literature/practice):

• Gene silencing: transient knockdown of human BRD4 mRNA via RISC‑mediated cleavage to study transcriptional regulation, enhancer function, and chromatin dynamics governed by BET bromodomains. Useful in dissecting super‑enhancer‑driven gene programs and cell cycle control in diverse cell systems.
• Pathway interrogation: compare BRD4 knockdown with chemical BET inhibition (e.g., JQ1) to distinguish catalytic bromodomain functions from scaffolding roles. Time‑course knockdowns enable mapping of primary versus secondary transcriptional responses.
• Synthetic lethality screens: deploy as part of combinatorial perturbation matrices to reveal genetic interactions with epigenetic modifiers, CDK9, or Mediator complex components (research use only).
• Assay endpoints: quantify knockdown by RT‑qPCR for BRD4 transcripts and by western blot for BRD4 protein isoforms; downstream readouts include nascent RNA labeling, ChIP‑qPCR/ChIP‑seq at super‑enhancers, and reporter assays.

Practical tips (general):

• Use a pooled set of 3–4 siRNAs at equimolar ratios to enhance on‑target efficacy and reduce off‑target noise.
• Optimize transfection conditions per cell line (lipid type, charge ratio, exposure time). Include non‑targeting and positive‑control siRNAs (e.g., PLK1) and a transfection control (e.g., siGLO) for benchmarking.
• Harvest RNA at 24–48 h and protein at 48–72 h post‑transfection for maximal effects. Validate strand specificity using sense/antisense controls where possible.

All uses are for research purposes only.

Reaction Conditions

Classical reaction condition parameters (solvent, catalysts, yields) are not applicable. For functional application of siRNA in cells, the following general transfection conditions are commonly effective (literature/practice; optimize per cell line):

• Dosing: 5–50 nM final siRNA concentration in culture, with many lines responding well to 10–25 nM when using modern lipid reagents. Use pooled siRNAs to limit off‑target effects.
• Complexation: dilute siRNA and lipid separately in serum‑free medium (e.g., Opti‑MEM), incubate 5–20 minutes to form complexes, then add to cells. Typical lipid:siRNA charge ratios follow vendor guidance for the transfection reagent.
• Timing: assess mRNA knockdown at 24–48 h and protein reduction at 48–72 h. For long experiments, consider re‑dosing at 72–96 h.
• Cell density: transfect at 40–70% confluence for adherent lines to balance viability and uptake; suspension lines may require electroporation.
• Controls: include non‑targeting siRNA, a positive control (e.g., PLK1) to gauge transfection efficiency, and mock controls. For BRD4, consider a chemical inhibitor (e.g., JQ1) as a pharmacological comparator.
• Readouts: RT‑qPCR for BRD4 transcripts, western blot for BRD4 isoforms, and functional assays (e.g., Pol II Ser2 phosphorylation, enhancer RNA levels).

Item-specific recommended conditions are not provided; refer to the product CoA/Spec Sheet and your transfection reagent’s protocol.

Safety & Handling

GHS/SDS item-specific data:

• Signal Word: Not specified for this item; refer to SDS.
• H‑Statements: Not specified for this item; refer to SDS.
• GHS Classification: Not specified for this item; refer to SDS.
• Pictograms: Not specified for this item; refer to SDS.

General laboratory safety guidance for siRNA reagents (literature/practice):

• Hazards: siRNAs are non-volatile, non-flammable polyanionic biopolymers with low intrinsic acute toxicity; principal risks arise from contamination (RNases), endotoxin, or transfection reagents used alongside. Avoid aerosol generation when handling lyophilizates or dried films.
• PPE: laboratory coat, nitrile gloves, and eye protection. Change gloves frequently to minimize RNase contamination. Use RNase‑free consumables.
• Handling: work in a clean area; wipe surfaces and tools with RNase decontamination solution. Use filtered tips. For cell work, maintain aseptic technique.
• Incompatibilities: strong nucleases (RNase A and environmental RNases), prolonged exposure to elevated temperature, and extreme pH (<6 or >9) that can promote hydrolysis; avoid repeated freeze–thaw cycles.
• First aid (general): in case of skin/eye contact, rinse with water. If inhaled as dust/aerosol, move to fresh air. If ingested, rinse mouth with water. Seek medical attention as appropriate; consult SDS for authoritative instructions.
• Waste: dispose of aqueous nucleic acid solutions according to institutional biosafety policies; decontaminate with appropriate solutions if required. Transfection mixtures may be subject to additional disposal requirements based on the reagent used.

Solvent Selection

This product is an siRNA duplex set, not a small‑molecule solute intended for organic solvent systems. Classical solvent selection paradigms (polarity, dielectric constant, miscibility) are not typically applicable.

General reconstitution media considerations (literature/practice):

• Primary diluents: RNase‑free water (nuclease‑free) is widely used for initial resuspension. Low‑salt buffers such as 1× TE (10 mM Tris‑HCl, 1 mM EDTA, pH 7.5–8.0) can improve long‑term stability by chelating divalent cations that catalyze RNA hydrolysis. Item‑specific instructions are not provided; follow CoA/Spec Sheet if available.
• Working buffers: for transfection, siRNA is commonly diluted in serum‑free, RNase‑free media (e.g., Opti‑MEM) prior to complexation with lipid reagents; final complexes are then added to complete growth media per reagent instructions (general guidance).
• Incompatible media: avoid organic solvents (MeOH, EtOH, DMSO) for stock solutions, as they can denature transfection complexes and negatively impact cells. Minimize exposure to strong acids/bases that promote RNA backbone cleavage.
• Concentration strategy: prepare a concentrated master stock (e.g., 10–50 μM, literature/practice) to reduce freeze–thaw cycles; exact recommended concentration for this item is not specified.

If uncertainty exists, prepare parallel small aliquots in RNase‑free water and in TE (pH 7.5–8.0) and assess performance—select the medium that preserves activity in your assay system.

Storage & Reconstitution

Item-specific information from Product Data:

• Storage Conditions: Store at −20 °C.
• Shipped In: Ice chest + Ice pads.

Additional general guidance (literature/practice; not item‑specific):

• Upon receipt: centrifuge briefly to collect material at the bottom of the tube. Inspect for damage or condensation from shipping.
• Reconstitution: dissolve each siRNA duplex in RNase‑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., 10–50 μM). Exact recommended concentration for this item is not specified; refer to CoA/Spec Sheet.
• Aliquoting: prepare single‑use aliquots to avoid repeated freeze–thaw. Use RNase‑free tubes and filtered tips.
• Storage after reconstitution: store aliquots at −20 °C (short to mid‑term) protected from light; for extended storage, −80 °C is common in research practice. Avoid more than 3–5 freeze–thaw cycles.
• Handling: maintain a clean, RNase‑free environment; wear fresh gloves, and decontaminate surfaces and tools with RNase removal solution. Thaw on ice, mix gently (do not vortex vigorously), and keep on ice during setup.
• Stability: lyophilized siRNA is typically stable for months at −20 °C in a desiccated environment; in solution, stability improves in slightly basic pH with EDTA. Item‑specific shelf life is not specified; consult the CoA.

Research Use Note: For research use only.

Structure & Identity

Item-specific identifiers (CAS, SMILES, InChIKey, exact sequences) are not specified for this item; refer to CoA/Spec Sheet.

General/literature description of the material type:

• The product is a pre-designed siRNA set targeting human BRD4 (BET family bromodomain-containing protein 4), typically supplied as a collection of 2–4 double‑stranded RNA duplexes directed at non-overlapping regions of the BRD4 mRNA (literature/general description).
• Typical siRNA architecture (literature): 19–21 bp duplex with 2‑nt 3′ overhangs (commonly dTdT), 5′-phosphate on the antisense strand, and optional proprietary chemical stabilizations to enhance nuclease resistance and reduce immune activation. Exact sequence, modifications, and length for this item are not specified.
• Structural features (general):
  • Functional class: small interfering RNA (RNA duplex, polyanionic nucleic acid).
  • Key moieties: ribose-phosphate backbone, nucleobases (A, U, G, C); may include 2′-O‑methyl or phosphorothioate linkages depending on design (not specified for this item).
  • Stereochemistry: native ribose centers are chiral; the duplex adopts A-form helical geometry under physiological ionic strength.
• Target gene: BRD4, human (HGNC:13573), mRNA reference sequences e.g., NM_058243 variants (for context; exact targeted transcript regions not specified).

Molecular formula and molecular weight: Not specified for this item; refer to CoA/Spec Sheet. For context, individual siRNA duplexes typically have MW in the ~13–15 kDa range depending on length and modifications (literature/general).

Synthetic Utility

This product is a biological reagent (siRNA set) and is not a synthetic building block for chemical transformations. Classical synthetic utility discussions (e.g., functional group interconversions, named reactions) do not apply.

General utility in experimental design (literature/practice):

• Chemical biology tool: enables targeted, reversible reduction of BRD4 levels to probe causality in gene regulation, epigenetic state, and pathway wiring. Complements small‑molecule BET inhibitors by removing protein rather than transiently blocking bromodomains.
• Methodological integration: pairs with ChIP‑seq, PRO‑seq/GRO‑seq, ATAC‑seq, RNA‑seq, and phospho‑proteomics to connect chromatin occupancy with transcriptional outcomes. Facilitates CRISPRi benchmark comparisons for knockdown depth versus speed.
• Orthogonal validation: combining independent siRNAs (from the set) reduces risk of off‑target artifacts; rescue with siRNA‑resistant BRD4 or domain mutants strengthens mechanistic conclusions.

From a chemistry operations standpoint, oligonucleotide synthesis, purification, and analytical methods (phosphoramidite chemistry, HPLC/PAGE, MS) underpin siRNA manufacture, but end‑users typically receive ready‑to‑use material. No item‑specific synthetic details are provided here.

Target Specificity

Only item-specific information may be listed here.

• Target gene/protein, siRNA sequences, isoform coverage, and predicted off‑target assessments: Not specified for this item; refer to CoA/Spec Sheet.

General note: pre‑designed siRNA sets typically include multiple duplexes targeting distinct regions of the intended mRNA (here: human BRD4). Users often pool the duplexes or test individually to identify the most effective sequence in their system.

Frequently Asked Questions

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.