These modifications alter the natural structure of oligonucleotides to enhance nuclease resistance and stability in biological environments. The changes also enable precise conjugation with targeting molecules and improve pharmacokinetic properties, making them essential for developing effective therapeutic oligonucleotides and functional biomaterials.
Key applications include but are not limited to: therapeutic oligonucleotides, delivery system conjugation, and site-specific cleavage.
Backbone & Linkage Modifications
Backbone and linkage modifications are engineered alterations to the natural phosphate-sugar backbone of oligonucleotides. These changes are primarily designed to enhance nuclease resistance, thereby improving stability in biological environments, or to introduce site-specific cleavage properties and conjugation handles for advanced applications. Such modifications are critical for the development of robust therapeutic oligonucleotides and functional biomaterials.
Backbone Details
| Sub-category | Name (full) | Abbreviation / Code | Product Type | Applies to | Position | Function & mechanism (including like products) | Typical applications |
| Phosphorothioate (PS) | Phosphorothioate linkage | PS | Like | DNA / RNA | Any position | Replacement of one non-bridging oxygen in the phosphodiester backbone with sulfur. Confers resistance to nuclease degradation (exo- and endonucleases). Increases plasma half-life 10–100×. Slightly reduces hybridization affinity per modification; typically used at terminal positions. | ASO therapeutics, siRNA stabilization, aptamer stabilization, primer nuclease protection |
| 2′-Sugar modifications (RNA) | 2′-O-Methyl (2′-OMe) | 2′-OMe / mA mC mG mU | Like | RNA | Any position | Methyl group added to the 2′-OH position of ribose. Increases Tm, confers nuclease resistance, and reduces immunogenicity (TLR7/8 suppression). Standard modification in siRNA guide strands and ASO wings. | siRNA passenger strand, ASO wings, guide strand stabilization, immunogenicity reduction |
| 2′-Sugar modifications (RNA) | 2′-Fluoro (2′-F) | 2′-F / 2FA 2FC 2FG 2FU | Like | RNA | Any position | Fluorine substitution at the 2′ position. Highest RNA binding affinity among 2′ modifications. Also provides nuclease resistance. Used in alternating 2′-OMe/2′-F patterns in siRNA. | siRNA (alternating 2′-F/OMe design), aptamers, nuclease-resistant probes |
| 2′-Sugar modifications (RNA) | 2′-O-Methoxyethyl (MOE) | MOE-A / MOE-G / MOE-T / MOE-U / MOE-5-Me-C | Like | RNA | Any position (wings preferred) | Bulkier 2′ modification providing very high nuclease resistance and Tm elevation (~1–3°C per residue). FDA-approved modification in marketed ASO drugs (e.g., mipomersen, inotersen). Used in gapmer wings. | Gapmer ASO wings (FDA-approved design), clinical ASO therapeutics, long-acting siRNA |
| Locked Nucleic Acid (LNA) | Locked Nucleic Acid (LNA) | (+A)(+C)(+G)(+T) | Like | DNA / RNA | Any position (wings or probe positions) | Bicyclic sugar modification constraining ribose in 3′-endo conformation. Highest Tm increase among nucleic acid analogs (+4–8°C per LNA residue). Excellent nuclease resistance. Allows very short yet highly specific probes (8–12 nt). | LNA probes, miRNA inhibitors (antimiRs), gapmer ASOs, very-short high-affinity probes |
| Constrained ethyl (cEt) | Constrained Ethyl BNA (cEt) | cEt-A / cEt-G / cEt-T / cEt-5-Me-C | Like | DNA / RNA | Wing positions in gapmer | Next-generation LNA analog with an ethyl bridge instead of methylene. Provides LNA-like Tm elevation with improved tolerability profile for therapeutic applications. Used in Ionis Pharmaceuticals' generation 2.5 ASO chemistry. | Clinical-grade gapmer ASO, improved tolerability over LNA in therapeutic programs |
| Other modified sugars | 2′-Arabinonucleotide (araF / 2AFA) | 2AFA 2AFC 2AFG 2AFU | Like | RNA | Any position | Arabino-configured fluorinated nucleotide (FANA). Mediates RNase H cleavage similar to DNA, used in antisense applications where FANA replaces the DNA gap. | FANA-modified gapmer ASO, RNase H-dependent antisense |
| Other modified sugars | GNA (Glycol Nucleic Acid) | GNA-A/C/G/T/U | Like | RNA | Limited positions | Acyclic nucleic acid analog with propylene glycol backbone. High binding affinity to RNA despite simpler structure. Explored in siRNA guide strand design. | siRNA research, acyclic backbone nucleic acid research |
| Other modified sugars | TNA (Threose Nucleic Acid) | TNA-A/C/G/T/U | Like | RNA | Limited positions | Backbone replaces ribose with L-threose. Highly nuclease-resistant. Used as a model for prebiotic chemistry and as a drug delivery scaffold. | Nuclease-resistant probes, origin-of-life research, therapeutic scaffold exploration |
| Other modified sugars | Hexitol Nucleic Acid (HNA) | Hd-A/C/G/U | Like | RNA | Limited positions | Cyclohexane backbone HNA modification. Very high thermal stability and nuclease resistance. Explored in antisense and aptamer applications. | Nuclease-stable antisense, aptamer stabilization |
Modification: PS
Download the order form "Tsingke_DNA_Order Form.1.1.1.250815.csv" for DNA modifications or "Tsingke_RNA_Order Form.1.1.1.250815.csv" for RNA modifications below and email it to info@tsingke.com.cn, or "Send Your Request" to submit your inquiry online. Please refer to "Tsingke_DNA_Modification List_1.1.1.250815.csv" or "Tsingke_RNA_Modification List_1.1.1.250815.csv" sheet to paste special base and internal modification codes in your sequence.
These are chemical alterations made to the natural sugar-phosphate backbone of oligonucleotides. They are designed to enhance properties such as nuclease resistance, stability in biological environments, and the ability to attach other molecules or enable site-specific cleavage.
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