Rethinking The Oligonucleotide Backbone: A New Approach To RNA Therapeutic Design

By David R. Tabatadze, Ph.D., president and CEO, ZATA Pharmaceuticals, Inc.

As oligonucleotide therapeutics continue to mature, one constraint keeps resurfacing: the backbone itself.

For decades, innovation in RNA therapeutics has focused primarily on sequence design, target selection, and delivery systems. In contrast, the phosphodiester backbone — long treated as a largely fixed structural element — has received relatively limited attention, aside from a few modifications such as phosphorothioates, guanidine, and mesyl groups. Yet this backbone quietly governs many of the field’s most persistent challenges, including cellular uptake, toxicity, and endosomal escape.

A growing body of research suggests that this assumption may be limiting.

Recent work, including platform-level efforts from companies like ZATA Pharmaceuticals, is reframing the backbone not as a passive scaffold but as a programmable feature that can be engineered with the same intentionality as sequence or chemistry.

Some researchers recognized the importance of backbone neutralization and cationization through the introduction of amino-terminated groups at internucleoside phosphates. However, a major obstacle remained. Until 2008, when we synthesized our first amidites, there was significant skepticism regarding the feasibility of such compounds. Amino-terminated phosphotriesters were long considered non-synthesizable.

For example, Serge L. Beaucage and colleagues explored amino-terminated butyl and pentyl esters as alternatives to the cyanoethyl protecting group, highlighting both the interest in this concept and the associated synthetic challenges.

What enabled our success was the specific design of our backbone-modifying groups. Beyond providing advantageous therapeutic properties, these designs imparted sufficient stability to allow efficient synthesis and purification of ZATA’s modified oligonucleotides.

Moving Beyond Phosphorothioates

Traditional backbone modifications, particularly phosphorothioates, have played a critical role in stabilizing oligonucleotides and enabling clinical translation. But they come with trade-offs: nonspecific protein binding, toxicity concerns, and limited tunability.

The emerging question is not whether backbone modification works but whether it can be done more precisely.

Instead of relying on uniform backbone substitutions, newer approaches explore site-specific and modular backbone engineering, where chemical properties can be tuned along the length of the oligonucleotide.

This shift opens the door to a more nuanced design space, one where different regions of the same molecule can carry distinct physicochemical properties.

A Programmable Backbone

At the center of this approach is the idea that key therapeutic properties — charge, hydrophobicity, and functionalization — can be programmed directly into the backbone.

Our work illustrates one implementation of this concept using modified amidite monomers. These building blocks allow chemists to:

• selectively neutralize or redistribute backbone charge
• introduce controlled cationic character
• incorporate hydrophobic elements at defined positions
• attach functional groups along the backbone rather than at terminal ends.

The result is not a single new chemistry but a design framework — one that treats the oligonucleotide as a modular system rather than a fixed structure.

This kind of control has potential implications across several known bottlenecks in RNA therapeutics.

Why Backbone Control Matters

Many of the challenges in oligonucleotide drug development stem from mismatches between molecular properties and biological environments.

For example:

• Endosomal escape remains inefficient for many modalities, limiting intracellular activity.
• Cellular uptake is often constrained by charge and membrane interactions.
• Delivery system compatibility depends heavily on molecular packaging behavior.
• Circulation time and biodistribution are influenced by both charge and hydrophobicity.

Backbone engineering introduces a new lever to address these constraints, – not by changing the delivery vehicle but by altering the molecule itself.

One notable aspect of this strategy is the ability to mask or redistribute negative charge, a defining feature of nucleic acids that contributes to both stability and delivery challenges. By modulating charge locally or globally, researchers can explore how oligonucleotides behave in biological systems with fewer electrostatic constraints.

Preserving What Already Works

A central concern with any backbone modification is whether it disrupts core oligonucleotide function.

Hybridization, structural integrity, and protein interactions are all highly sensitive to changes in backbone chemistry. Historically, more aggressive modifications have risked compromising these fundamentals.

The newer generation of approaches attempts to balance innovation with preservation.

In the case of phosphotriester-based designs, the goal is to maintain:

• canonical Watson–Crick base pairing
• native nucleic acid geometry
• compatibility with existing sugar and base chemistries.

If successful, this would allow backbone modifications to enhance performance without undermining the mechanisms that make oligonucleotides effective in the first place.

Compatibility As A Design Constraint

Another practical consideration is whether new chemistries can integrate into existing workflows.

Unlike entirely new modalities, backbone engineering approaches that rely on modified amidites can be incorporated into standard solid-phase oligonucleotide synthesis. This lowers the barrier to experimentation and adoption, particularly for groups already working across antisense, siRNA, or CRISPR-based systems.

Importantly, this also allows backbone modifications to be explored within established therapeutic frameworks, rather than requiring entirely new development pipelines.

From Uniform Molecules To Heterogeneous Design

Perhaps the most significant conceptual shift is this: oligonucleotides no longer need to be chemically uniform along their length.

Instead, they can be designed as heterogeneous molecules, where different segments perform different roles:

• one region optimized for target binding
• another for stability
• another for cellular uptake or trafficking.

This mirrors trends seen in other areas of drug development, where modularity and multifunctionality are increasingly central to design.

The Remaining Questions

Despite the promise, several open questions remain.

• Translatability: How do these modifications behave across different tissues and disease contexts?
• Manufacturing consistency: Can complex, position-specific designs scale reliably?
• Safety profiles: Does long-term modulation of charge and hydrophobicity introduce new risks?
• Regulatory clarity: How will increasingly complex backbone chemistries be evaluated?

These are not trivial challenges, and they will likely determine how broadly backbone engineering is adopted.

A Shift In Where Innovation Happens

What’s becoming clear is that innovation in RNA therapeutics is no longer confined to sequence or delivery alone.

The backbone, once considered fixed, is emerging as a third axis of control.

Whether through platforms like ours, or other approaches still in development, the field is beginning to explore what happens when backbone properties become as programmable as sequence itself.

If that shift holds, it could redefine how oligonucleotides are designed, not just as carriers of genetic information but as finely tuned molecular systems engineered for performance in complex biological environments.

About The Author

David R. Tabatadze, Ph.D., is president and CEO of ZATA Pharmaceuticals, Inc., a clinical-stage biotech company based in Worcester, MA. He has a Ph.D. in oligotherapeutics and a master’s degree in organic chemistry. Tabatadze cofounded ZATA in 2008 and has been instrumental in the development of modern oligonucleotides with improved therapeutic properties. He is also a major architect in the development of oligotherapy and has been involved in various bio-science research and therapeutic development projects. Tabatadze’s contributions to the field of oligotherapy and his leadership at ZATA Pharmaceuticals have been recognized with honors, including being one of the two life sciences firms to win the New England Innovation Awards.