Nuclease protection · ligation · surface immobilization · gel embedding
Terminal Modifications
Modify the 5′ or 3′ terminus for nuclease protection, surface attachment, or to enable downstream enzymatic reactions.
| Category | Sub-category | Name (full) | Abbreviation / Code | Applies to | Position | Function & mechanism (EN — for website copy) | Typical applications |
| Terminal Modifications | 3′ end blockers | 3′ Inverted dT (InvdT / 3′-InvdT) | InvdT / Inv-dT | DNA / RNA | 3′ | 3′ to 3′ phosphodiester linkage blocks 3′ exonuclease degradation. Does not require a 3′-OH, preventing extension by DNA polymerases. Standard stabilization for primers and probes. | 3′ exonuclease protection, non-extendable primers, stabilized probes |
| Terminal Modifications | 3′ end blockers | 3′-ddC (Dideoxycytidine) | ddC | DNA / RNA | 3′ | Chain-terminating dideoxynucleotide blocking 3′ extension. Commonly used in Sanger sequencing dideoxy termination and as a primer 3′-blocker. | Sanger sequencing terminators, polymerase extension blocking, allele-specific PCR blockers |
| Terminal Modifications | 3′ end blockers | 3′-ECL | 3′-ECL | DNA | 3′ | Electrochemiluminescence label enabling signal generation in ECL-based detection platforms (e.g., Meso Scale Discovery). Enables highly sensitive low-volume immunoassay detection. | ECL-based immunoassays, Meso Scale Discovery platform, high-sensitivity detection |
| Terminal Modifications | 5′ reactive groups | 5′-Acrydite | Acrydite | DNA / RNA | 5′ | Acrylamide group for direct copolymerization into polyacrylamide gels. Covalent attachment — survives gel denaturation. | Embedded oligo gels, in-gel hybridization, polyacrylamide bead functionalization |
| Terminal Modifications | 5′ reactive groups | 5′-CHO (Aldehyde) | CHO | DNA / RNA | 5′ | Reactive aldehyde for hydrazone or reductive amination conjugation. Used for site-specific coupling to hydrazide- or amine-functionalized surfaces and proteins. | Hydrazone conjugation, oligonucleotide-aldehyde surface coupling |
| Terminal Modifications | 5′ reactive groups | 5′-COOH (Carboxyl) | COOH | DNA / RNA | 5′ | Carboxyl group activated with EDC/NHS for amine coupling. Enables conjugation to amine-functionalized surfaces, nanoparticles, and proteins. | EDC/NHS surface coupling, nanoparticle functionalization |
| Terminal Modifications | 5′ reactive groups | 5′-CHCH (Alkyne) | CHCH | DNA / RNA | 5′ | Terminal alkyne for CuAAC click chemistry with azide partners. Complementary to azide-modified oligos or azide-labeled surfaces. | CuAAC click conjugation, oligonucleotide-surface attachment |
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