Chemical Modifications

Enhancing oligonucleotide therapeutics through strategic chemistry

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Start Your Project

Chemical Modifications

Enhancing oligonucleotide therapeutics through strategic chemistry

Start Your Project

Strategic Chemical Optimization for Therapeutic Success

The biological performance of therapeutic oligonucleotides—whether siRNAs or antisense oligos (ASOs)—depends not only on sequence, but also on the chemical modifications applied to their structure. Sugar, backbone, and terminal modifications can dramatically influence how an oligo behaves in vivo—shaping its stability, delivery efficiency, immunogenicity, and overall pharmacology.

While ADViRNA does not synthesize or design every chemical format in-house, we routinely test and evaluate chemically modified oligonucleotides provided by our partners. Our in vitro screening platforms allow us to assess how specific modifications affect biological performance, including knockdown potency, protein-level effects, and compatibility with delivery strategies.

Why Modifications Matter

Unmodified oligonucleotides are rapidly degraded in blood and tissue, poorly internalized by cells, and often fail to escape endosomes. Modifications are critical to overcoming these limitations and unlocking therapeutic potential.

Enhanced Nuclease Resistance

Enhanced Nuclease Resistance

Improve nuclease resistance in plasma and intracellular compartments for enhanced stability
Superior Target Affinity

Superior Target Affinity

Enhance target affinity and hybridization kinetics for optimized therapeutic
performance
Extended Circulation Time

Extended Circulation Time

Prolong circulation time through protein binding or charge modulation for sustained effect
Enhanced Nuclease Resistance

Enhanced Nuclease Resistance

Improve nuclease resistance in plasma and intracellular compartments for enhanced stability
Superior Target Affinity

Superior Target Affinity

Enhance target affinity and hybridization kinetics for optimized therapeutic performance
Extended Circulation Time

Extended Circulation Time

Prolong circulation time through protein binding or charge modulation for sustained effect
Reduced Toxicity

Reduced Toxicity

Reduce immune activation and toxicity for improved safety profiles and therapeutic windows
Targeted Delivery

Targeted Delivery

Enable targeted delivery via conjugation to ligands such as GalNAc, cholesterol, or peptides

Reduced Toxicity

Reduced Toxicity

Reduce immune activation and toxicity for improved safety profiles and therapeutic windows
Targeted Delivery

Targeted Delivery

Enable targeted delivery via conjugation to ligands such as GalNAc, cholesterol, or peptides

These benefits, however, are only meaningful when applied to sequences with proven biological activity. That’s why ADViRNA emphasizes sequence-first design, followed by chemical evaluation in a systematic, data-driven way.

Common Modifications of Therapeutic Oligonucleotides and Their Functions

Sugar Modifications Modification: 2'-O-Methyl (2'-OMe) Function: Improves nuclease resistance; reduces immune activation Modification: 2′-Fluoro (2′-F) Function: Enhances RISC loading; increases duplex stability Modification: 2'-O-Methoxyethyl Function: Extends half-life; boosts affinity Modification: Locked Nucleic Acid (LNA) Function: Increases target binding strength and specificity Modification: DNA (2'-H) Function: Enables RNase H activity in gapmer ASOs Modification: Other analogs (UNA, GNA, HNA) Function: May impact flexibility, resistance, or pharmacodynamics
Backbone Modifications Phosphorothioate (PS) Improves nuclease resistance and plasma protein binding PMO (Phosphorodiamidate Morpholino) Stable, uncharged; blocks translation Triazole, Borano, Thiophosphoramidate Specialized chemistries for custom delivery strategies
Sugar Modifications Modification: 2'-O-Methyl (2'-OMe) Function: Improves nuclease resistance; reduces immune activation Modification: 2′-Fluoro (2′-F) Function: Enhances RISC loading; increases duplex stability Modification: 2'-O-Methoxyethyl Function: Extends half-life; boosts affinity Modification: Locked Nucleic Acid (LNA) Function: Increases target binding strength and specificity Modification: DNA (2'-H) Function: Enables RNase H activity in gapmer ASOs Modification: Other analogs (UNA, GNA, HNA) Function: May impact flexibility, resistance, or pharmacodynamics
Backbone Modifications Phosphorothioate (PS) Improves nuclease resistance and plasma protein binding PMO (Phosphorodiamidate Morpholino) Stable, uncharged; blocks translation Triazole, Borano, Thiophosphoramidate Specialized chemistries for custom delivery strategies
Terminal Modifications & Conjugates Modification/Conjugate: GalNAc Function: Liver targeting via ASGPR Modification/Conjugate: Cholesterol Function: Enhances uptake and endosomal escape Modification/Conjugate: DCA (Docosanoic Acid) Function: Broad tissue exposure Modification/Conjugate: Vinyl Phosphonate Function: Increases in vivo stability of siRNA and enhances the in vivo efficacy and duration of the effect Modification/Conjugate: PEG, Biotin, Fluorophores Function: Modulate PK, enable imaging, or support assay readouts Modification/Conjugate: Antibody and Peptide Conjugates Function: Enable cell-specific or tissue-directed delivery Modification/Conjugate: Linkers / Spacers (e.g., C3, HEG) Function: Improve flexibility and accessibility

ADViRNA's Role in Modification Testing

At ADViRNA, our role in the modification process is both scientific and strategic. While we synthesize many common modification patterns in-house, such as various 2’-O-methyl and 2’-fluoro designs, phosphorothioates, etc., we work closely with clients to guide the selection and testing of modification strategies that make the most biological sense for their therapeutic goals.

For more complex or customized chemistries, we coordinate synthesis through trusted external partners.

Vials in ADViRNA lab meticulously being filled.

Scientific Guidance

Extensive scientific guidance based on internal expertise and peer-reviewed studies that outline how chemical modifications impact stability, delivery, and efficacy

ADViRNA scientist sits with a client for a consultation.

Strategic Consultation

Consultation on modification strategy based on delivery route, therapeutic tissue, and downstream application

Scientist pipetting in a lab at ADViRNA for the purpose of in vitro testing.

In Vitro Testing

In vitro testing of modified oligos using our standard screening platforms (qPCR, luciferase, ELISA, Western blot)

Photo of vials going through the process of comparative analysis at ADViRNA.

Analysis

Comparative analysis of modified versus unmodified candidates to refine therapeutic leads

Typically, we recommend introducing chemical modifications only after sequence and conjugate validation, allowing clients to optimize confirmed hits within a stable, proven framework. This structured approach accelerates decision-making while minimizing unnecessary complexity early in development.

Rational Chemistry, Guided by Biology

Our workflow reflects a biology-driven, stepwise approach to oligonucleotide development—one that balances speed, cost, and scientific rigor.

  1. Screen and validate siRNA/ASO sequences, often using simple, widely used modification patterns (such as alternating 2′-O-methyl and 2′-fluoro chemistries with phosphorothioate backbones). These formats are cost-effective, easy to synthesize, and compatible with most in vitro models—making them ideal for early candidate evaluation.

  2. Evaluate conjugates to determine the optimal delivery route and tissue targeting strategy.

  3. Apply and test more tailored chemical modification patterns in downstream studies to refine lead candidates for in vivo performance. At this stage, modifications can be optimized based on the delivery method, dosing route, target tissue, desired half-life, and immunogenicity profile.

This tiered approach allows clients to move quickly through early screening while still ensuring that lead candidates are ultimately optimized with the appropriate chemical features for translational success.

Let's Evaluate the Chemistry Behind Your Next Candidate

Whether you’re preparing a lead for in vivo studies or comparing chemical strategies for knockdown potency and safety, ADViRNA can help you test and refine your modifications based on sound data, not guesswork.

Contact Us

Let's Evaluate the Chemistry Behind Your Next Candidate

Whether you’re preparing a lead for in vivo studies or comparing chemical strategies for knockdown potency and safety, ADViRNA can help you test and refine your modifications based on sound data, not guesswork.

Contact Us

Chemical Modifications