SETMAR Human Pre-designed siRNA Set A

Cat. No.: S1460046

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

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

Tested applications, specific transfection protocols, recommended concentrations, and validated cell lines are not provided in the product data for this SKU.

• Item-specific protocols and any performance data: Not specified for this item; refer to CoA/Spec Sheet and the product’s SDS/technical datasheet.

For experimental setup, please follow your transfection reagent manufacturer’s instructions and standard institutional protocols for siRNA use.

Biological Roles

Target: Human SETMAR (also known as Metnase) — literature overview of gene function to contextualize knockdown studies.

• Domain architecture: Fusion of an N‑terminal SET histone methyltransferase domain with a C‑terminal mariner transposase-like domain (literature).
• Reported activities: Histone H3 methylation (e.g., H3K36-related marks in some contexts) and DNA end‑processing functions linked to the transposase domain (literature).
• Cellular roles: Implicated in non-homologous end joining (NHEJ), replication restart, and genomic stability pathways; interacts with DNA repair factors (literature).
• Experimental phenotypes: SETMAR depletion has been associated with altered DSB repair efficiency, changes in chromatin accessibility at break sites, and replication stress sensitivity in model systems (literature).

Caveats:

• Isoforms and cell-type specificity can influence outcomes; validate knockdown at both mRNA and protein levels.
• Off-target RNAi effects may confound phenotypes—use multiple independent siRNAs and rescue experiments where possible (general best practice).

Note: The above is general literature context for SETMAR biology and not item-specific performance claims.

Buffer Applications

siRNA handling relies on RNase-free aqueous buffers. No item-specific buffer composition is provided for this SKU.

Common buffer systems (literature/general):

• RNase-free water: For reconstitution and short-term working solutions.
• TE buffer (10 mM Tris·HCl, 0.1–1 mM EDTA, pH 7.5–8.0): Enhances stability during frozen storage by chelating divalent cations.
• HEPES-buffered saline (HBS) or Opti‑MEM: Frequently used during transfection complex formation per reagent instructions.

Practical tips:

• Maintain pH ~7.0–8.0; acidic conditions can promote depurination, while strong base accelerates RNA hydrolysis (literature).
• Use nuclease-free plastics and dedicated, cleaned benches; avoid Mg2+/Ca2+ in storage buffers unless required by downstream steps.

Item-specific recommendations (concentration, exact buffer): Not specified for this item; refer to CoA/Spec Sheet.

Green Alternatives

siRNA workflows are inherently aqueous and can be aligned with green chemistry and green lab principles.

• Solvent footprint: Aqueous buffers (water/TE/PBS) minimize VOC use compared with organic-solvent–intensive chemistries (general).
• Energy: Store at −20 °C as specified; consider shared cold storage and inventory control to reduce freezer load while maintaining stability.
• Reagents: Choose less hazardous transfection reagents where feasible; some lipid formulations are less irritant than cationic polymers (balance efficacy vs. hazard; literature).
• Waste: Segregate bio/chemical waste; neutralize and minimize bleach/chaotropic salts. Prefer non-DEPC sterilization when compatible (e.g., filtration) to reduce hazardous residues (general).

Illustrative comparison (general):

• Lipid-based transfection vs. solvent-heavy methods: Lipids enable aqueous complexation without chlorinated solvents; however, they may have cytotoxicity at higher doses.
• RNase-free water vs. denaturing agents: Favor RNase-free water/TE for routine handling instead of high concentrations of phenol/guanidinium used in extraction workflows.

Pharmaceutical Uses

This product is for research use only.

General R&D context (literature):

• siRNA reagents are widely used in preclinical discovery to validate targets, map pathways, and assess mechanism of action in cell lines and ex vivo models before considering other modalities.
• Formulation research may explore delivery systems (lipid nanoparticles, polymers, conjugates) in vitro; this SKU is not supplied with or validated for clinical use.

Regulatory/compendial status:

• No pharmacopeial status or clinical-grade certification is indicated. Item-specific compliance information is not specified; refer to CoA/Spec Sheet for any available QC descriptors.

Do not use in humans or for diagnostic purposes.

Physical Properties

Item-specific physicochemical specifications are not provided.

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Solubility: siRNA is highly soluble in aqueous, RNase-free buffers (literature). Exact solubility for this item is not specified.
• Extinction/OD quantitation: Typical RNA quantification at 260 nm (A260 = 1 ≈ ~40 µg/mL for single‑stranded RNA; duplex factors vary) (literature). Item-specific extinction coefficient is not specified.
• pKa/logP/refractive index: Not applicable/reported for large polyanionic oligonucleotides (literature).
• Melting temperature (Tm): Sequence- and salt-dependent; typically 60–85 °C for 21–23‑mer duplexes under physiological salt (literature). Not specified for this item.
• Hygroscopicity: Oligos can absorb moisture when lyophilized; store desiccated (general guidance).

Notes:

• Do not treat the above as item specifications; they are general literature values for siRNA. For definitive values (e.g., concentration, OD, mass, formulation), consult the item’s CoA/Spec Sheet.

Quality & Grades

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

General notes on siRNA quality (literature):

• Common purification levels: Desalted, cartridge, PAGE, or HPLC. Higher purity (PAGE/HPLC) typically improves knockdown consistency and reduces off-targets.
• Identity/quality controls may include: OD260 concentration, duplex integrity (native PAGE/HPLC), mass confirmation (MALDI/ESI), and endotoxin/bioburden testing for cell-based use. Specific QC for this item is not specified.
• Stabilizers/modifications: Some siRNAs include 2′‑O‑Me/2′‑F bases or phosphorothioates to enhance stability; presence/extent for this item is not specified.

Implications for use:

• For sensitive applications (primary cells, long incubations), prefer higher-purity, low-endotoxin siRNA. Confirm the exact purification and any modifications from the CoA/Spec Sheet for this SKU.

Reaction & Applications

This product is intended for RNA interference (RNAi)-mediated knockdown of human SETMAR in cell-based systems (research use only).

Key application contexts (literature/general):

• Gene function studies: Reduce SETMAR transcript levels to assess roles in DNA repair and chromatin regulation in human cell lines.
• Pathway mapping: Evaluate effects on non-homologous end joining markers, replication stress responses, and chromatin marks downstream of SET domain activity.
• Assay modalities: qRT‑PCR for mRNA, Western blot for protein, reporter assays for pathway readouts, and imaging for DNA damage foci (e.g., γH2AX).

Practical tips (general):

• Use multiple siRNA duplexes targeting distinct SETMAR regions to mitigate off-targets and confirm on-target effects; “Set A” nomenclature suggests a panel, but the number/sequences are not specified for this item.
• Optimize transfection conditions in each cell line: reagent type, siRNA dose (commonly 5–50 nM), and exposure time (24–96 h) (literature guidance).
• Include controls: non-targeting siRNA, positive knockdown control, and transfection reagent only.
• Verify knockdown kinetics: peak mRNA reduction often precedes maximal protein depletion.

Manufacturer application text: Not provided in product data; users should consult the product page or CoA for any item-specific application notes.

Reaction Conditions

While not a chemical reaction, RNAi transfection has empirically optimized conditions. The following are literature-based general guidelines; item-specific instructions are not provided.

• Cell lines: Adherent lines (e.g., HEK293, HeLa, U2OS) and suspension lines can be used with appropriate transfection methods (lipid/electroporation).
• Dose: Common working concentrations range 5–50 nM siRNA duplex in culture; start with a 3-point titration (e.g., 5, 10, 25 nM) to balance efficacy and cytotoxicity (literature).
• Complexation: Form complexes in serum-free medium (e.g., Opti‑MEM) per transfection reagent protocol; incubate 10–30 min at room temperature before adding to cells (literature).
• Incubation/time course: Assess mRNA knockdown at 24–48 h and protein reduction at 48–96 h; extend as needed for stable proteins (literature).
• Controls: Non-targeting siRNA, positive silencing control, and mock transfection.
• Readouts: qRT‑PCR (ΔΔCt), Western blot/ELISA, functional assays (DNA repair reporters, γH2AX foci) relevant to SETMAR pathways.

Note: Exact recommended conditions, sequences, and the number of duplexes in “Set A” are not specified for this item; consult the CoA/Spec Sheet and your chosen transfection reagent documentation.

Safety & Handling

GHS/SDS details are not provided in the product data; handle per institutional biosafety and chemical hygiene practices.

• GHS classification, signal word, pictograms, H-statements: Not specified for this item; refer to SDS.
• Primary hazards: siRNA itself is generally considered low hazard but is susceptible to RNase degradation. Transfection reagents used alongside may be irritant/corrosive—consult their SDS (literature/general).
• PPE: Laboratory coat, gloves, eye protection. Use RNase-free techniques (dedicated tips/tubes, clean benches) to prevent degradation (general guidance).
• Handling:
  • Work on ice when preparing dilutions to limit nuclease activity.
  • Use certified RNase-free water/buffers; avoid DEPC in solutions intended for cell culture unless properly removed (general guidance).
  • Avoid repeated freeze–thaw; aliquot stocks.
• Incompatibilities: RNases (from skin, dust, unclean plastics), nuclease-contaminated solutions, prolonged room‑temperature exposure (general guidance).
• First aid (overview): In case of contact with eyes/skin, rinse with water. If inhaled or ingested, follow institutional first-aid protocols and seek medical attention; present SDS (general guidance).

Always consult the official SDS for authoritative hazard, exposure limits, and emergency procedures.

Solvent Selection

As an oligonucleotide, this siRNA set is formulated/reconstituted in aqueous media.

• Preferred solvents: RNase-free water, TE buffer (10 mM Tris·HCl, 0.1–1 mM EDTA, pH ~7.5–8.0), or nuclease-free PBS for some applications (literature). Item-specific recommended buffer is not specified.
• Compatibility: Fully miscible with water; incompatible with organic solvents for stock solutions (which may denature or precipitate RNA). Short exposures to serum-containing media are typical during transfection (literature).
• Practical selection:
  • Long-term stock: RNase-free water or TE; EDTA chelates divalent cations that catalyze RNA hydrolysis (literature).
  • Working solutions: Serum-free transfection medium during complexation, then complete medium post-transfection (per transfection reagent guidance).

Comparison (general):

• Water (RNase-free): Minimal components; best for broad use.
• TE buffer: Improved stability for frozen stocks; avoid high EDTA if downstream requires divalent cations.
• PBS: Convenient isotonic diluent; avoid Mg2+/Ca2+ which may promote degradation.

Storage & Reconstitution

• Storage conditions (from product data): Store at −20 °C.
• Shipping: Ice chest + ice pads (from product data).

Reconstitution (general guidance; item-specific instructions are not provided):

• Use RNase-free water or buffer (e.g., TE, pH ~7.5–8.0) to prepare a concentrated stock. The exact target concentration for this SKU is not specified; choose a convenient laboratory standard and document it.
• Vortex gently and briefly spin down; allow complete dissolution on ice.
• Aliquot immediately into RNase-free tubes to avoid repeated freeze–thaw cycles.

Storage after reconstitution (general):

• Short term (≤1 week): 2–8 °C.
• Long term: −20 °C to −80 °C. Avoid frost-free freezers and minimize freeze–thaw events.
• Protect from RNase contamination; use dedicated, clean pipette tips and tubes.

Appearance, stabilizers, and exact formulation: Not specified for this item; refer to CoA/Spec Sheet.

Structure & Identity

This product is a gene-silencing reagent: a pre-designed siRNA set targeting human SETMAR (SET domain and mariner transposase fusion) transcripts.

• SKU: S1460046
• Product name: SETMAR Human Pre-designed siRNA Set A
• Target gene: SETMAR (Homo sapiens) — from product name
• Chemical identifiers (CAS, CID, InChIKey, SMILES): Not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

General structural description (literature):

• Small interfering RNA (siRNA) reagents are typically double-stranded RNA duplexes of ~19–27 base pairs with 2-nt 3′ overhangs (often dTdT) and 5′ phosphates on guide/passenger strands.
• May include chemical stabilizations (e.g., 2′-O-methyl, 2′-F, phosphorothioate linkages) to improve nuclease resistance; specific modifications for this item are not specified.
• Functional groups: polyanionic phosphate backbone; ribose sugar (β-D-ribofuranose) and nucleobases (A, U, G, C).

Synthetic Utility

Not typically applicable. This product is a functional gene-silencing reagent rather than a synthetic building block or reaction substrate.

General note (literature):

• Oligonucleotides can serve as templates or primers in molecular biology reactions (PCR, RT), but siRNA duplexes are designed for RISC-mediated mRNA cleavage and are not employed as reagents in chemical synthesis.

For practical value, see the Reaction & Applications and Reaction Conditions tabs, which focus on RNAi use rather than chemical synthesis.

Target Specificity

• Product type: Pre-designed siRNA set (duplexes) — from product name
• Target gene: SETMAR — from product name
• Species reactivity: Human (Homo sapiens) — from product name
• Number of siRNA duplexes, individual sequences, target exon/isoform coverage, and off-target analysis: Not specified for this item; refer to CoA/Spec Sheet.

Notes:

• Pre-designed siRNA sets typically include multiple non-overlapping duplexes to enhance the likelihood of robust knockdown and facilitate on-target confirmation (literature, general). Item-specific composition is not provided here.

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.