Oligonucleotide Design
Delivering targeted, rational, and biologically sound RNA therapeutics design services to accelerate your drug discovery with confidence
Oligonucleotide Design
Delivering targeted, rational, and biologically sound RNA therapeutics design services to accelerate your drug discovery with confidence
siRNA Design Services
Our proprietary siRNA design algorithm, developed in partnership with the Khvorova Lab and published in Nucleic Acids Research, was the first prediction tool trained specifically on chemically modified, cholesterol-conjugated siRNAs. Unlike traditional tools built around unmodified, naked duplexes, ours is optimized for the structural and biochemical constraints of modern self-delivering RNA therapeutics.
The algorithm takes the following into account:
- Positional base preferences that correlate with functional activity
- Chemical compatibility, including known intolerance of certain modifications
- Sequence accessibility, especially AU-rich flanking regions that enhance efficacy
- Target site features predictive of functional RISC loading and cleavage
Validated across multiple independent datasets, this tool has demonstrated up to 80% positive predictive power for self-delivering, cholesterol-conjugated siRNAs. Optional filters allow us to prioritize:
Transcript selectivity
Cross-species homology
Off-target minimization
Compatibility with downstream assays and delivery formats
Antisense Oligonucleotide (ASO) Design Services
We also provide ASO design services using a validated, open-source prediction algorithm based on the ViennaRNA package. This framework models RNA secondary structure and helps prioritize sites with high hybridization potential and functional accessibility.
While the tool itself is open-source, our added value lies in biological context and expert filtering— selecting optimal ASO sites based on target region architecture, conservation, and the specific goals of your experiment.
Data-Driven Design, Biologically Refined
Once candidate sequences are generated, we conduct a collaborative review session to visualize designs across your target transcript(s). Together, we evaluate each sequence’s placement and potential impact, considering:
- Alternative splicing and isoform-specific targeting
- Polyadenylation variants and transcript architecture
- Overlapping regulatory elements or UTR features
- Cross-species alignment for in vitro/in vivo continuity
Following this review, we deliver a curated list of prioritized oligonucleotides, ready for use in any downstream application.
Why Design with ADViRNA?
Rational design is where the best therapeutics begin, and our process is built around partnership. We prioritize scientific rigor, transparent communication, and client-first flexibility, providing a clear advantage over generic design tools or black-box vendors.
Clients appreciate our:
- Consistent communication from consultation to delivery
- Deep domain expertise in RNA biology and gene regulation
- Optional add-ons like RNA sequencing to confirm transcript accuracy
- No-pressure approach: You can use our designs with any synthesis or screening provider
That said, if you choose to partner with us for downstream services, we’ll ensure a seamless handoff into screening, analytics, and in vivo validation, with no lost context along the way.
Partner with ADViRNA
As a boutique CRO specializing in RNAi, we offer fast turnaround times, exceptional flexibility, and seamless collaboration from sequence design to in vivo validation. Whether you’re looking to develop a tool compound, optimize delivery systems, or advance a therapeutic, ADViRNA provides the precision and performance your project demands.
Partner with ADViRNA
As a boutique CRO specializing in RNAi, we offer fast turnaround times, exceptional flexibility, and seamless collaboration from sequence design to in vivo validation. Whether you’re looking to develop a tool compound, optimize delivery systems, or advance a therapeutic, ADViRNA provides the precision and performance your project demands.