High-purity, chemically modified RNA oligonucleotides tailored for gene silencing and RNAi therapeutic development.
Built on optimized T7 RNA polymerase-driven in vitro transcription systems, the service supports the production of small interfering RNAs (siRNAs), microRNA mimics, anti-miR oligonucleotides, and short hairpin RNA templates. Each oligonucleotide can be further modified with terminal or internal chemical groups including 2′-O-methyl, phosphorothioate linkages, locked nucleic acids (LNA), and 5′/3′ cholesterol conjugates—choices that directly influence stability, delivery efficiency, and specificity.
Typical applications include functional validation of candidate genes, target identification in RNAi screens, and preclinical development of RNA-based therapeutics, particularly for CNS malignancies such as glioma. All production is performed under RNase-free conditions and includes rigorous quality control to verify sequence identity, purity, and modification efficiency.
Modification patterns are selected based on the intended use—minimal stabilization for transient in vitro studies, or full chemical protection for prolonged in vivo circulation. Our team can also advise on conjugate selection (e.g., cholesterol, GalNAc, or cell-penetrating peptide) to improve cellular uptake in hard-to-transfect cell types.
Key Features
Custom Sequence Design
Our design team evaluates target mRNA sequences using RNAi specificity algorithms and thermodynamic rules to select siRNA or miRNA sequences with maximal on-target potency and minimal off-target potential. For miRNA mimics, seed region matching and predicted Argonaute loading are assessed. GC content, secondary structure, and off-target seed matches are checked, and multiple candidates are typically tiled across the target. We also accept pre-specified sequences from customer designs.
Chemical Modification Suite
To improve nuclease resistance and thermal stability, we can incorporate a range of chemical modifications at defined positions: 2′-O-methyl (2′-OMe) and 2′-fluoro (2′-F) on ribose, phosphorothioate (PS) backbone linkages, terminal inverted abasic caps, and LNA or bridged nucleic acid (BNA) residues. The modification pattern is customized per project—from minimal stabilization (2–4 terminal PS) to fully modified siRNA duplexes for extended in vivo half-life.
Fluorescent and Conjugation Labels
For cellular uptake studies, biodistribution tracking, or FRET-based assays, we offer terminal or internal labeling with FAM, Cy3, Cy5, or biotin. Additional conjugation handles (amine, thiol, azide) are available for downstream coupling to nanoparticles, antibodies, or other carriers. Labeling efficiency is verified by fluorescence measurement or mass spectrometry and typically exceeds 80–90% for standard fluorophores.
Scalable Synthesis from µg to mg
Synthesis scale is scoped per project, from microgram quantities for preliminary screening to multi-milligram yields for in vivo animal studies or pilot-scale production. Purification methods (PAGE, HPLC, or a combination) are selected based on length, modification load, and purity requirement. All batches include a detailed QC report documenting yield, purity (≥90% by UV/A260), and modification confirmation.
Product Types
We produce a range of small RNA product types to support gene silencing and miRNA research:
Small Interfering RNA (siRNA): Standard 19–21 bp duplex with 2-nt 3′ overhangs; can be fully or partially modified for stability. Delivered as annealed duplex or separate strands for custom annealing.
MicroRNA Mimics: Double-stranded oligonucleotide that mimics a mature endogenous miRNA; guide strand loaded into RISC to repress target mRNAs. Available with chemically stabilized passenger strand to reduce off-target effects.
Anti-miR Oligonucleotide (AMO): Single-stranded inhibitor designed to bind and sequester endogenous microRNAs; fully phosphorothioated and often 2′-O-methyl or LNA modified for improved affinity and nuclease resistance.
Short Hairpin RNA (shRNA) Template: DNA template encoding a stem-loop structure that is transcribed by Pol III into shRNA; can be synthesized as a linear double-stranded oligo for vector cloning or as a ready-to-transfect RNA hairpin.
Chemically Modified Asymmetric siRNA (asiRNA): An siRNA variant with shortened passenger strand (15–19 nt) designed to reduce off-target activity while retaining guide-strand activity. Particularly useful for alleles with single-nucleotide specificity.
Workflow
Each synthesis project follows a structured four-phase workflow, from consultation to QC release.
Project Consultation and Sequence Design: We review the target sequence, required modification pattern, scale, and downstream application. For new designs, we perform bioinformatic analysis to optimize guide selection, assess off-target potential, and recommend modification chemistry. Scoping parameters are documented in a project SOW.
Template Construction and In Vitro Transcription: DNA templates are constructed with T7 or dual-promoter sequences. In vitro transcription is performed under RNase-free conditions using optimized ribonucleotide mixes. For modified RNAs, corresponding modified NTPs are incorporated during transcription.
Chemical Modification and Duplex Annealing: Post-transcription chemical conjugation steps (e.g., fluorescent labels, cholesterol, or GalNAc) are introduced as specified. Single strands are annealed to form duplexes if required by the project. Annealing efficiency is verified by non-denaturing gel electrophoresis.
Purification, QC, and Delivery: Oligonucleotides are purified by PAGE or HPLC to remove template DNA, excess nucleotides, failure products, and salts. QC includes UV absorbance (A260/A280 ratio), denaturing gel electrophoresis, and mass spectrometry (MALDI-TOF or LC-ESI-MS) for identity and modification verification. A QC report and storage recommendations accompany each shipment.
Quality Assurance
Every synthesis batch is subjected to a standard QC panel that includes UV spectrophotometry (A260 measurement for yield and purity ratio A260/A280 ≥ 1.8), denaturing polyacrylamide gel electrophoresis (PAGE) for size and strand integrity, mass spectrometry (MALDI-TOF or LC-ESI-MS) for molecular weight confirmation and verification of chemical modifications, and HPLC purity analysis for labeled or extensively modified RNAs. Fluorescent labeling efficiency is verified by fluorescence measurement against a standard curve; efficiency is reported as a percentage of labeled product.
For every project, a lot-specific QC report is issued documenting the measured parameters. The report includes gel images, MS spectra, and purity traces. All production records are retained for traceability. Long-term storage recommendations (typically -80°C in nuclease-free water or ethanol precipitation) are provided with each shipment.
Why Choose Us
Design Expertise with RNAi Specificity Algorithms: Our team uses established RNAi design tools (including proprietary filters for seed-match off-targets) to maximize on-target knockdown and reduce unintended effects.
Comprehensive Chemical Modification Options: We support a wide range of stabilizations, labels, and conjugations—from simple 2′-OMe/PS to complex multi-label constructs—all customizable per project needs.
Rigorous QC with Multiple Validation Methods: Each batch is tested by UV, gel, and mass spectrometry. Modification incorporation and labeling efficiency are quantified, not assumed.
Dedicated Project Management with Scientific Support: You receive a named scientific contact at project start with milestone review calls and email response within one business day.
Backed by Creative Biogene: All projects are delivered under Creative Biogene's ISO-aligned quality system, with dedicated project management, milestone-based reporting, and full intellectual property protection for your data.
Commonly Studied Cell Types
Our siRNA/miRNA synthesis supports gene silencing studies across a broad range of cell lines and primary cultures. The following examples illustrate typical model systems used in RNAi projects; final selection is scoped per project.
Glioblastoma Cell Lines: U87, U251, T98G, LN229—widely used in functional genomics and drug sensitivity studies for glioblastoma multiforme.
Neuroblastoma Cell Lines: SK-N-SH, IMR-32—models for neuroblastoma and neuronal differentiation; often used in miRNA and siRNA functional validation.
Primary Glioma Cultures: Patient-derived primary glioma cells preserve the molecular heterogeneity of the original tumor and are preferred for translational RNAi studies.
Patient-Derived Xenograft (PDX) Models: PDX-derived cell lines maintain tumor microenvironment features and are used for evaluating siRNA/miRNA therapeutic efficacy in a more clinically relevant context.
Contact Us
Whether you need a chemically stabilized siRNA duplex, a fluorescently labeled anti-miR, or a custom conjugate for targeted delivery, the scientific team at Creative Biogene can help you design the right synthesis and modification strategy. Reach out to discuss a tailored solution for your next project.
