# Antisense Oligonucleotides > Antisense oligonucleotides in MBBS Biochemistry: RNase H gapmers, splice switching, nusinersen for SMA, inotersen, chemical modifications and delivery. - Canonical URL: https://prepelephant.com/topics/mbbs/biochemistry/antisense-oligonucleotide - Exam / course: MBBS · Subject: Biochemistry - Publisher: PrepElephant (https://prepelephant.com) — Prepared and reviewed by the PrepElephant Academic Review Team - First published: 2026-10-02 - Last updated: 2026-10-02 - How to cite: "Antisense Oligonucleotides", PrepElephant, https://prepelephant.com/topics/mbbs/biochemistry/antisense-oligonucleotide ## Direct answer An antisense oligonucleotide is a short synthetic strand — typically 18 to 25 bases — engineered to base-pair with one specific RNA and change its fate, and everything depends on two design choices. Gapmers carry an unmodified DNA core flanked by modified RNA wings: RNase H1 recognises the RNA-DNA duplex and cuts the RNA, silencing the gene. Fully modified splice-switching oligomers do not cut anything; they physically block splice sites or silencer motifs — the mechanism of nusinersen, which binds the ISS-N1 site in SMN2 pre-mRNA so that exon 7 is retained and functional SMN protein is produced in spinal muscular atrophy. Naked DNA would last minutes; phosphorothioate backbones, 2'-O-methyl and morpholino chemologies make the drugs survive. ## What you must remember - **Two mechanisms, cleanly separated:** RNase H1-mediated cleavage (gapmers — mipomersen against apoB for homozygous familial hypercholesterolaemia; inotersen against transthyretin in hereditary amyloidosis) versus steric-block splice modulation (nusinersen, eteplirsen). - **Nusinersen specifics:** 2'-O-methoxyethyl phosphorothioate chemistry, intrathecal administration, four loading doses then maintenance roughly every four months; transforms the natural history of infantile-onset SMA when started early. - **Eteplirsen:** a phosphorodiamidate morpholino (PMO) restoring the reading frame of Duchenne dystrophin by exon-51 skipping. - **Why chemistry is everything:** phosphodiester DNA is shredded by nucleases and triggers innate immunity; phosphorothioate substitution resists nucleases and binds plasma proteins, extending half-life. - **First in class:** fomivirsen, 1998, against CMV retinitis — the first approved antisense drug, later withdrawn as its indication faded; it remains the historical one-liner. - **ASO versus siRNA:** antisense works through RNase H or steric blocking with a single strand; siRNA (patisiran for ATTR) loads Argonaute in RISC to slice the target — a mechanism pair examiners explicitly contrast. - **Delivery logic:** intrathecal for spinal cord targets, GalNAc conjugation for hepatocyte uptake — the liver is the easy organ, the brain the hard one. - **Safety flags:** thrombocytopenia and renal monitoring with inotersen; injection-site reactions with subcutaneous gapmers. ## Nusinersen, from genotype to injection Spinal muscular atrophy deletes or disables SMN1, yet every patient carries SMN2, a near-copy that differs by a C-to-T transition causing exon 7 to be skipped in most transcripts — a truncated, rapidly degraded protein. Nusinersen binds the ISS-N1 intronic silencer just upstream of exon 7, physically preventing repressor splicing factors from sitting there, so the spliceosome includes exon 7 and full-length SMN is produced from the backup gene. SMN2 copy number explains disease severity (infants with two copies are worst affected) and predicts response — a genotype-therapy correlation students can recite end to end. Because the oligomer does not cross the blood-brain barrier, it is given by lumbar puncture into the CSF, reaching motor neurons directly. Distinguish it from onasemnogene abeparvovec, which delivers a functional SMN1 by viral vector — the ASO is RNA therapy, not gene therapy, and saying so cleanly is the mark of a prepared candidate. Access in India remains limited by cost, a real-world caveat worth one measured sentence. ## Where students slip The first slip is mechanical: "antisense always degrades RNA" — splice-switching oligomers never touch RNase H; nusinersen blocks, it does not cut, and this is precisely why it needs full modification rather than a DNA gap. The second is lumping nusinersen with gene therapy, corrected above. The third is forgetting why modifications exist at all — a question that invites the nuclease-and-immunity answer, not just a list of chemical names. Fourth, ASO versus siRNA: single-stranded RNase-H/steric-block acting alone versus double-stranded RISC-dependent slicer — if an examiner supplies patisiran, name the siRNA mechanism unprompted. The intrathecal route is not a detail; it is the answer to "why not oral", and connecting BBB impermeability to route of administration shows clinical reasoning, not recall. ## Frequently asked questions ### What are the two mechanisms of antisense oligonucleotide action? RNase H1 cleavage of the RNA-DNA duplex in gapmers, and steric blockade — masking splice sites or translation starts — by fully modified oligomers without any cleavage. ### Why must antisense oligonucleotides be chemically modified? Unmodified DNA is rapidly degraded by nucleases and can activate innate immune sensors; phosphorothioate, 2'-O modifications and morpholinos confer stability and tune pharmacokinetics. ### What does nusinersen target, and how is it given? It binds the ISS-N1 site of SMN2 pre-mRNA to promote exon 7 inclusion, and it is given by intrathecal injection because it cannot cross the blood-brain barrier. ### How does an siRNA drug differ from an antisense oligonucleotide? siRNA is double-stranded and works through the RISC-Argonaute slicer complex, while ASOs are single strands acting via RNase H or steric blockade. ### Which was the first approved antisense drug? Fomivirsen, licensed in 1998 for cytomegalovirus retinitis in AIDS patients and later withdrawn from the market as its indication disappeared.