Antisense oligonucleotides (ASOs) are specialized synthetic molecules designed to interfere with genetic instructions to treat disease. These short strands of nucleic acid are engineered to specifically bind to messenger RNA (mRNA), the transient copy of a gene that carries instructions for protein production. By neutralizing or destroying the mRNA transcript, ASOs effectively prevent the cell’s machinery from manufacturing the corresponding protein, a process known as gene silencing. This technology reverses the effects of diseases caused by the overproduction of a harmful protein or the presence of a faulty genetic message.
Among the various types of ASOs, the gapmer design is a potent and widely used therapeutic strategy. Gapmers are characterized by a unique chemical architecture that harnesses a natural cellular pathway to achieve permanent gene knockdown. This approach offers a highly targeted method for regulating gene expression, providing new avenues for treating a range of conditions from rare genetic disorders to common chronic diseases.
The Specialized Structure of Gapmer Molecules
The functionality of a gapmer ASO is linked to its tripartite structure: a central “gap” region flanked by two “wings.” The molecule is typically a short strand, usually between 15 and 22 nucleotides in length. This chimeric design, combining different chemical units, provides the necessary balance between target binding, stability, and therapeutic action.
The central gap is composed of unmodified deoxyribonucleotides, the same chemical units found in DNA. This stretch of DNA, often eight to ten nucleotides long, is the functional core of the molecule, as it triggers the gene-silencing mechanism. The flanking wings are composed of chemically modified nucleotides distinct from natural DNA or RNA, introduced to enhance the molecule’s pharmacological properties.
Common modifications in the wings include 2′-O-Methoxyethyl (MOE) or Locked Nucleic Acid (LNA) units. These chemical groups significantly increase the thermal stability and binding affinity of the gapmer to its target mRNA sequence. The modified wings also protect against degradation by nucleases, allowing the gapmer to persist longer within the cell and enabling its repeated use in the silencing process.
The RNase H Mechanism of Gene Silencing
The therapeutic power of the gapmer design is activated once the molecule locates and binds to its complementary target mRNA. This binding forms a heteroduplex—a double-stranded structure composed of the synthetic gapmer and the natural mRNA. This specific hybrid architecture initiates the core gene-silencing action.
The central DNA gap region, paired with the target mRNA, creates a unique DNA/RNA hybrid substrate. This substrate is recognized by the endogenous cellular enzyme Ribonuclease H1 (RNase H1). RNase H1 functions to degrade the RNA component of an RNA-DNA duplex. When the enzyme encounters the gapmer-mRNA hybrid, it specifically cleaves the phosphodiester bonds along the bound mRNA strand.
This cleavage rapidly fragments the target mRNA, destroying the template needed for protein synthesis. Since the mRNA is degraded, the ribosome is prevented from translating the genetic code into a functional protein, achieving gene silencing. RNase H1 only acts on the DNA-RNA hybrid and cannot cleave the chemically modified wings. The wings, protected by their MOE or LNA modifications, remain intact while the enzyme destroys the target mRNA.
Once the mRNA is cleaved, the RNase H1 enzyme dissociates, and the intact gapmer ASO is released to bind to another target mRNA molecule. This catalytic recycling mechanism means a single gapmer molecule can degrade multiple copies of the target mRNA, significantly amplifying the therapeutic effect. The gapmer is not consumed in the reaction but acts as a highly specific trigger, leading to a sustained reduction in the production of the unwanted protein.
Current Therapeutic Uses and Research Focus
The ability of gapmer ASOs to achieve targeted and durable gene silencing has led to their successful translation into approved medicines. This drug class is suited for diseases where the goal is to reduce the concentration of a specific protein. The high specificity of gapmers minimizes off-target effects, making them a precise tool in molecular medicine.
A number of gapmer drugs have received regulatory approval for various indications.
Approved Gapmer Examples
Mipomersen (Kynamro) treats homozygous familial hypercholesterolemia by targeting the mRNA for apolipoprotein B.
Inotersen (Tegsedi) targets the transthyretin gene to treat hereditary transthyretin amyloidosis, a disease characterized by the buildup of misfolded protein deposits.
Tofersen, approved for a specific form of amyotrophic lateral sclerosis (ALS), targets the mRNA for the superoxide dismutase 1 (SOD1) gene. This gapmer is delivered directly into the central nervous system, demonstrating the capacity to reach previously inaccessible tissues.
Volanesorsen targets apolipoprotein C-III mRNA to reduce triglycerides in familial chylomicronemia syndrome, highlighting utility in managing complex metabolic disorders.
The therapeutic landscape for gapmers continues to expand rapidly, focusing on neurological and rare genetic disorders.
Ongoing research explores the potential of gapmers in treating a wide array of conditions, including various forms of cancer and infectious diseases, by targeting genes that promote tumor growth or viral replication. The field is continuously working on next-generation chemistries, exploring new wing modifications and delivery systems to enhance potency, improve tissue distribution, and reduce the required dosage.