CIPC Human Pre-designed siRNA Set A

Cat. No.: C1465484

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Panoramica

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

The following is a general siRNA transfection workflow; adapt to your cell model and transfection reagent. Item-specific sequences, concentrations, and validation data are Not specified for this item.

• Preparation:
  • Thaw siRNA aliquots on ice. Work RNase-free. Prepare cells to be 40–60% confluent at transfection.
• Complex formation (example):
  • Dilute siRNA in serum-free medium to 2× desired final concentration (e.g., 20 nM for a 10 nM final).
  • In a separate tube, dilute transfection reagent per manufacturer’s instructions (e.g., 1–3 µL reagent per well of a 24-well plate, literature range).
  • Combine equal volumes, gently mix, and incubate 10–20 min at room temperature.
• Transfection:
  • Replace cell medium with fresh complete medium or follow reagent-specific guidance.
  • Add complexes dropwise; rock plate gently. Incubate 4–6 h before optional medium change.
• Controls:
  • Include non-targeting siRNA, a positive control siRNA, and a mock condition.
• Post-transfection analysis:
  • Harvest RNA at 24–48 h for RT–qPCR; harvest protein at 48–96 h for immunoblot.
  • For circadian studies, synchronize cells (e.g., 50% serum shock for 2 h, literature) and monitor reporters/targets over time.
• Troubleshooting (general):
  • Low knockdown: Optimize siRNA dose, reagent amount, and cell density; verify siRNA integrity by gel.
  • Cytotoxicity: Reduce reagent amount or siRNA dose; ensure antibiotics are absent during complexing.

Biological Roles

This section summarizes general/literature information about the human CIPC gene and protein; it is provided for research context and is not product-specific.

• Gene/protein: CIPC (CLOCK-interacting pacemaker). Interacts with core circadian regulators, notably CLOCK, and has been implicated as a negative regulator within the circadian transcriptional feedback loops (literature).
• Function (literature): CIPC can modulate CLOCK/BMAL1-mediated transcriptional activity, contributing to the fine-tuning of circadian gene expression. It may act as a repressor by interacting with the transcriptional machinery and/or influencing protein stability and complex assembly.
• Expression and regulation: CIPC expression shows tissue distribution consistent with circadian control pathways; its levels and activity may be temporally regulated in certain models (literature). Detailed expression profiles are context- and model-dependent.
• Pathways: Circadian rhythm, transcriptional regulation, and potential crosstalk with metabolism and cell-cycle timing have been suggested (literature).
• Research utility of CIPC knockdown: Silencing CIPC enables interrogation of clock periodicity, phase, and amplitude in cellular circadian models; downstream effects can be characterized by time-course qPCR of clock-controlled genes and luciferase reporter assays under synchronized conditions (e.g., serum shock), providing mechanistic insight into feedback dynamics.
• Orthologs: CIPC homologs are present across vertebrates, enabling cross-species comparative studies; however, this product targets the human transcript specifically.

Buffer Applications

Conventional chemical buffer design (pH buffering capacity/ionic screening) is not the main focus for this product. Instead, consider buffers compatible with siRNA stability and transfection.

• Resuspension buffers (general/literature):
  • Nuclease-free water (pH ~7–8) for maximum versatility.
  • Low-EDTA TE (10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0) helps chelate Mg2+/Ca2+ that can activate RNases; avoid high EDTA if complexing with cationic lipids.
• Working dilution media:
  • Serum-free, antibiotic-free culture medium for complex formation with lipid reagents (5–30 min at room temperature), then add to cells in complete medium.
• Storage buffers (general):
  • Short-term (days to weeks): RNase-free water or 1× TE at -20°C.
  • Long-term (months): Aliquoted stocks at -80°C in 1× TE or water; avoid repeated freeze–thaw.
• Electrophoresis/analysis:
  • For QC, native or denaturing PAGE in TBE/UREA systems can assess integrity and duplex formation (general practice).
• Additives:
  • Include RNase inhibitors only where protocol requires; they are not a substitute for RNase-free technique.
• Item-specific buffer recommendations: Not specified for this item; refer to CoA/Spec Sheet.

Green Alternatives

Although siRNA use is inherently aqueous and low in volatile organics, the associated workflows can be optimized for greener laboratory practice. The following are general, non–item-specific recommendations.

• Reduce hazardous reagents:
  • Prefer lipid-based transfection reagents with lower cytotoxicity and minimal solvent content; avoid chlorinated solvents for sterilization or cleanup.
  • Use ethanol or isopropanol for surface disinfection instead of halogenated agents where appropriate.
• Minimize plastic and waste:
  • Plan plate layouts to reduce dead volumes and disposable tip usage; adopt multi-dispense pipetting and reservoir reuse when sterility permits.
  • Choose low-retention, recyclable plastics; collect tips/tubes for specialized recycling streams if available.
• Energy efficiency:
  • Consolidate freezer storage; maintain -80°C units at -70°C when validated, which can halve energy use (institutional policy dependent).
  • Batch experiments to reduce incubator/hood runtime.
• Substitute materials (when compatible):
  • Use phosphate-free detergents for equipment cleaning.
  • Select aqueous, non-toxic dyes for viability/readouts in place of organic solvent–intensive stains.
• Comparative note (general): siRNA workflows typically have a lower solvent footprint than organic-synthesis workflows. The largest impacts are from cold-chain logistics and single-use plastics; focus improvements there. No item-specific green alternative is applicable for a targeted siRNA set.

Pharmaceutical Uses

This is a research-grade, pre-designed siRNA set intended for laboratory use only.

• Regulatory/compendial status: Not specified for this item; no pharmacopeial monograph is implied.
• Formulation/excipient role: Not applicable—this product is not supplied as a pharmaceutical excipient. It is a gene-silencing research reagent.
• Process development relevance (general): Insights from siRNA knockdown studies can inform target validation and mechanism-of-action research in discovery settings. Any translation to therapeutic development requires separate, GMP-grade materials, defined sequences, extensive safety/pharmacology, and regulatory oversight, none of which are implied by this listing.
• Endotoxin/bioburden: For cell-based assays, low endotoxin is preferred; item-specific limits Not specified for this item; refer to CoA/Spec Sheet.
• Sterility: Not sterile unless stated; filter or aseptically handle as needed for sensitive applications (general guidance).

Physical Properties

Item-specific physico-chemical specifications are not provided in the Product Data and should be confirmed from the CoA/Spec Sheet. Below are general/literature properties and handling notes for siRNA oligonucleotides:

• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet. (Typical 21-mer siRNA duplexes are ~13–14 kDa total, literature.)
• Molecular formula: 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 aqueous buffer, literature.)
• Solubility (literature): Freely soluble in nuclease-free water and low-salt buffers (e.g., 10 mM Tris, pH 7–8). Avoid divalent cations without chelators due to nuclease activation.
• pKa/logP: Not applicable in the traditional sense; highly polar polyanionic biopolymers (literature).
• UV absorbance (literature): Strong at 260 nm; use A260 to quantify. Use strand-specific extinction coefficients if provided by supplier.
• Thermal stability (literature): Duplex melting temperature (Tm) depends on length, GC content, sequence, and modifications. Typical 21-mer siRNA Tm ~55–75°C in standard buffers.
• Refractive index, density, BP/MP: Not applicable/reported for solid oligonucleotides; Not specified for this item.
• Hygroscopicity (literature): Lyophilized siRNA can be mildly hygroscopic; protect from ambient moisture to maintain accurate concentration.

Quality and Grades

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
• Typical oligonucleotide quality attributes (general, not item-specific):
  • Purity methods: Desalting, cartridge purification, HPLC, or PAGE. Higher stringency (HPLC/PAGE) reduces truncated species and can improve knockdown consistency.
  • Identity confirmation: MALDI-TOF/ESI-MS, capillary electrophoresis, and analytical HPLC.
  • Quantitation: OD260 with sequence-specific extinction coefficients.
  • Residual salts/solvents: Assessed by conductivity and MS; low salt is preferred for transfection performance.
• What “pre-designed set” implies (general): Multiple distinct siRNA duplexes per target gene, each designed with rules that consider target accessibility, seed-region off-target minimization, and thermodynamic asymmetry to favor guide-strand loading.
• Stabilizers/modifications: If present, they can enhance nuclease resistance (e.g., 2′-OMe/2′-F, terminal phosphorothioates). Presence/extent for this item: Not specified; refer to CoA/Spec Sheet.
• Documentation to request for lot release (recommendation):
  • Synthesis report including purification method, analytical chromatogram, and mass data.
  • Sequence disclosure or masked IDs with target site information, and any chemical modifications.
  • RNase-free certification and endotoxin level if relevant for sensitive cells.

Reaction and Applications

As an siRNA set, this product is intended for RNA interference–based knockdown of human CIPC. Chemical reaction chemistry is not applicable; instead, focus on functional genomics applications.

• Principal application (general):
  • Transient sequence-specific silencing of CIPC mRNA via RISC-mediated cleavage and/or translational repression.
• Use cases in research (examples):
  • Dissecting the role of CIPC in circadian rhythm regulation and CLOCK/BMAL1-dependent transcription.
  • Validating CIPC as a node in gene networks via loss-of-function studies.
  • Phenotypic screening: Using a multi-siRNA set to identify on-target phenotypes while controlling for off-targets.
• Practical tips (general):
  • Test each siRNA individually and as pooled mixes; pooling can average sequence-specific off-target effects.
  • Optimize transfection reagent, cell density, and siRNA dose; assess cytotoxicity independently (e.g., using a viability assay) to avoid confounding knockdown readouts.
  • Measure knockdown at mRNA level by RT–qPCR at 24–48 h; confirm at protein level by immunoblot at 48–96 h (dependent on protein half-life).
  • Include controls: non-targeting siRNA, positive control siRNA (to a housekeeping or reporter), and mock transfection.
• Off-target mitigation (general): Lower siRNA concentration, chemical modifications (if provided), and seed region analysis can reduce off-target activity.
• Transfection formats: Adherent/suspension cells, reverse or forward transfection, 6- to 384-well plates for screening.

Reaction Conditions

While not a chemical reaction reagent, successful siRNA-mediated knockdown depends on optimized transfection and culture conditions. The following are general, literature-based guidelines and should be empirically optimized per cell type.

• Cell density: Typically 30–70% confluency at transfection time for adherent cells; suspension cells should be in exponential growth.
• siRNA dose (general ranges): 1–50 nM final concentration; many cell lines respond well at 5–20 nM when using efficient lipid reagents. Start with a 3-point titration (e.g., 2.5, 10, 25 nM).
• Complexation: Mix siRNA with transfection reagent in serum-free medium; incubate 10–30 min at room temperature to form lipoplexes.
• Incubation: Add complexes to cells and incubate 4–6 h before medium change (depending on reagent), or leave in complete medium if reagent supports it.
• Readouts: Assess mRNA at 24–48 h; protein at 48–96 h, considering CIPC protein turnover (literature generalization).
• Controls: Non-targeting siRNA, positive control siRNA, and transfection-only controls.
• Temperature/atmosphere: Standard mammalian culture conditions (37°C, 5% CO2) unless cell-type specific.
• Replicates/statistics: Use biological triplicates and technical duplicates; include time-course if circadian endpoints are measured.
• Item-specific recommended conditions: Not specified for this item; refer to CoA/Spec Sheet.

Safety and Handling

• GHS hazard classification, signal word, pictograms, H-statements: Not specified for this item; refer to SDS.
• General safety (literature/good practice):
  • Handle using aseptic, RNase-free technique to avoid degradation (wear gloves; use RNase-free tubes, filtered tips).
  • siRNA is not volatile and typically presents low acute hazard; nonetheless, avoid inhalation of powders/aerosols. Do not ingest or inject. For research use only.
  • Personal protective equipment: laboratory coat, disposable nitrile gloves, safety glasses. Change gloves frequently to minimize RNase contamination.
• Incompatibilities (general):
  • RNases (ubiquitous on skin/surfaces); decontaminate with RNase-inactivating solutions (e.g., 0.1% DEPC-treated water followed by autoclave, or commercial RNase removers). Avoid repeated freeze–thaw.
  • Strong acids/bases and nucleases that can hydrolyze/degrade RNA.
• First-aid overview (general):
  • Skin/eye contact: Rinse with water; remove contaminated clothing; seek medical attention if irritation persists.
  • Inhalation: Move to fresh air; seek medical attention if symptoms occur.
  • Ingestion: Rinse mouth; seek medical attention.
• Spill response (general): Avoid dust formation; wipe with damp RNase-free towels; dispose of per institutional guidelines.
• SDS: Consult the product-specific Safety Data Sheet for authoritative hazard and response information.

Solvent Selection

This product is an siRNA set; conventional organic solvent selection is not typically applicable. Focus on nuclease-free aqueous media.

• Recommended resuspension media (general/literature):
  • Nuclease-free water (RNase/DNase-free), pH ~7–8.
  • 1× TE or TE-like low-EDTA buffer (e.g., 10 mM Tris-HCl, 0.1–1 mM EDTA, pH 7.5–8.0) to chelate divalent cations that can activate nucleases.
  • For in vitro transfection, dilute working stocks in serum-free, antibiotic-free medium during complexation with transfection reagent, then add to complete medium after 10–30 min complexing (follow reagent manufacturer’s guide).
• Solvent compatibility (general): Avoid organic solvents (MeOH, DMSO) unless required by a protocol; they can affect transfection efficiency and cell viability. If DMSO is used in screening, keep final DMSO ≤0.1–0.5% (literature) to minimize cytotoxicity.
• pH/Ionic strength considerations: Moderate ionic strength (e.g., PBS) is acceptable for storage of aliquots; however, avoid Mg2+/Ca2+ unless EDTA is present.
• Filtration: If sterility is required, filter through low-protein-binding 0.22 µm filters after dilution; avoid filtering highly concentrated oligo solutions due to adsorption losses.

Storage and Reconstitution

• Storage conditions (item-specific): Store at -20°C. Shipment: Ice chest + ice pads (as provided in Product Data).
• Stability (general/literature): Lyophilized siRNA is stable for months at -20°C to -80°C if kept dry and protected from light. In solution, stability is enhanced at -20°C to -80°C; avoid repeated freeze–thaw cycles.
• Reconstitution (general guidance; item-specific concentrations Not specified):
  • Spin down the tube briefly to collect contents.
  • Add nuclease-free water or low-EDTA TE buffer to achieve a convenient stock (e.g., 20–100 µM, literature). Mix gently; avoid vigorous vortexing that can shear or aerosolize.
  • Allow to sit on ice for 10–15 min to fully dissolve. Verify concentration by A260 using the extinction coefficient if provided.
• Aliquoting:
  • Prepare single-use aliquots to avoid freeze–thaw. Use RNase-free, low-binding tubes.
• Short-term storage:
  • 2–8°C for hours to a day during setup; -20°C for days to weeks.
• Long-term storage:
  • -80°C for months. Protect from moisture. For duplexes supplied single-stranded, anneal per vendor instructions (item-specific status Not specified for this item).
• Thawing:
  • Thaw on ice, flick to mix, quick spin, and keep on ice during setup.
• Item-specific stabilizers, formulation, appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Research use note: For research use only.

Structure and Identity

• Item-specific identifiers (CAS, InChIKey, SMILES, exact sequence, length, chemical modifications, molecular formula, molecular weight): Not specified for this item; refer to CoA/Spec Sheet.
• Product type: Pre-designed small interfering RNA (siRNA) set targeting human CIPC (CLOCK-interacting pacemaker) mRNA; “Set A” typically comprises multiple distinct duplexes designed to the same gene to improve the chance of efficient knockdown (general/literature).
• Structural features (general for siRNA):
  • Double-stranded RNA duplexes, usually ~19–27 bp with 2-nt 3′ overhangs (commonly dTdT) to enhance RISC loading (literature).
  • Phosphodiester backbone; optional stabilizing modifications (e.g., 2′-OMe, 2′-F, phosphorothioates) may be present depending on design; item-specific presence/positions Not specified for this item.
  • Sense and antisense strands are complementary; antisense (guide) strand directs RISC to the target CIPC transcript (general mechanism).
• Target gene: CIPC (human). Gene symbol: CIPC; aliases: CLOCK-interacting pacemaker (literature).
• 2D description in words (general): Two antiparallel ribonucleotide strands hybridized via Watson–Crick base pairing, with ribose sugars (2′-OH) and canonical bases (A, U, G, C), forming a short A-form duplex suitable for RISC incorporation.
• Intended identity verification (general approaches): Mass spec of oligos, analytical HPLC/PAGE purity profiles, and functional knockdown of CIPC mRNA by qPCR/Western (not item-specific).

Synthetic Utility

Traditional organic synthesis utility does not apply. Instead, consider experimental design utility in molecular and cell biology.

• Functional utility (general):
  • Enables targeted loss-of-function studies for the human CIPC gene without permanent genomic alteration.
  • Facilitates pathway mapping by evaluating downstream transcriptional and phenotypic effects upon acute CIPC depletion.
• Experimental design advantages:
  • Use of multiple siRNAs (Set A) allows cross-validation of on-target phenotypes; concordance across distinct duplexes strengthens causal inference.
  • Pooling at equimolar ratios can increase knockdown robustness at lower total siRNA concentration, reducing off-targets from any single sequence (literature).
• Orthogonal confirmation:
  • Combine with CRISPRi, shRNA, or rescue experiments (overexpression of siRNA-resistant CIPC) to confirm specificity (general best practices).
• Downstream assays:
  • RT–qPCR for CIPC and clock gene panels, immunoblotting for protein levels, luciferase reporters for circadian output, and imaging-based phenotypic assays.
• Limitations (general):
  • Transient effect with variable duration depending on cell type and turnover.
  • Potential off-target effects mediated by seed-region pairing; mitigate via dose optimization and design selection.

Target Specificity

• Target gene: Human CIPC (CLOCK-interacting pacemaker). Species specificity: Homo sapiens (general based on product name).
• Design: Pre-designed siRNA Set A; typically includes multiple distinct duplex sequences targeting different regions of the CIPC mRNA to enhance the probability of robust knockdown (general). Exact sequences and target sites are Not specified for this item; refer to CoA/Spec Sheet.
• Off-target considerations (general):
  • Seed-mediated off-targeting can affect transcripts with 3′UTR complementarity to positions 2–8 of the guide strand.
  • Use low effective concentrations and, where possible, confirm with at least two independent siRNAs showing concordant phenotypes.
• Cross-reactivity:
  • Human-specific designs may or may not cross-react with orthologous transcripts in other species depending on sequence conservation; without disclosed sequences, cross-species reactivity is unknown for this item.
• Validation strategies (general):
  • RT–qPCR for CIPC mRNA reduction and Western blot for CIPC protein decrease.
  • Rescue experiments with siRNA-resistant CIPC cDNA to demonstrate on-target action.
• Item-specific validation data: Not specified for this item; refer to CoA/Spec Sheet.