Backbone & Linkage Modifications

Service Details of Backbone & Linkage Modifications

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.

Phosphorylation: Adds a phosphate group to the 5' end of an oligonucleotide. This is essential for enzymatic ligation reactions (e.g., connecting DNA fragments with T4 DNA ligase) or for specific labeling protocols.

Phosphorothioate (PS): Replaces a non-bridging oxygen in the phosphate backbone with sulfur. This is the most important modification for therapeutic oligonucleotides (like ASOs and siRNA) because it dramatically increases resistance to nucleases (stability in blood/serum) and improves tissue distribution.

Inverted-dT: Attaches a deoxythymidine to the 3' end upside-down. This physically blocks the 3' end, preventing enzymes from adding or removing nucleotides. It is crucial for blocking degradation in applications like microarrays or FISH.

5'- (E)-Vinylphosphonate (EVP): A backbone modification that improves stability and helps trigger gene silencing mechanisms more effectively.

Maleimide: Reacts specifically and rapidly with thiol groups (-SH). This is the go-to chemistry for attaching oligonucleotides to cysteine residues on proteins or to other thiolated molecules.

N-Acetylgalactosamine (GalNAc): A sugar molecule that targets the liver. It binds to a receptor on liver cells, making it essential for many modern siRNA and ASO drugs.

2′-O-hexadecanoyl (Hd): A long fatty acid chain added to the RNA sugar. Improves cell penetration and delivery, similar to cholesterol.

Cholesterol: Attaches a cholesterol molecule to the oligonucleotide. Helps it hitch a ride into cells by associating with lipids and cell membranes.

Aldehyde: Reacts with amine groups (-NH₂). This is commonly used to label amine-containing molecules or for immobilizing oligonucleotides onto amine-coated surfaces.

Alkyne & Azide: This is the classic pair for CuAAC ("click") chemistry. They react together in the presence of a copper catalyst to form a stable triazole linkage. Great for general conjugation in non-living systems.