Chart of Modifications
Chart of Oligonucleotide Modifications
This chart provides a quick reference to the main oligonucleotide modifications, their properties, and applications. Use it to compare options and find the modifications relevant to your oligo design. Detailed information is available on the Modifications page.
| Modification | 5' | internal | 3' | Type | Method | Function 1 | Function 2 | Noteworthy |
|---|---|---|---|---|---|---|---|---|
| 2'-F-A/C/G/U | - | X | - | RNA | CEP | - | - | Backbone |
| 2'-MOE-A/mC/G/T | - | X | - | RNA | CEP | - | - | Backbone |
| 2'-OMe-5-Methyl-C | - | X | - | RNA | CEP | - | Epigenetic | Backbone |
| 2'-OMe-A/C/G/U | - | X | - | RNA | CEP | - | Epigenetic | Backbone |
| -3'-3'- (Directional Switch) | - | X | - | - | - | - | - | Backbone |
| 3'-O-Propargyl-5-Methyl-dC | - | - | X | DNA | SP | Click | CuAAC | - |
| 3'-O-Propargyl-A/C/G/U | - | - | X | RNA | SP | Click | CuAAC | - |
| -5'-5'- (Directional Switch) | - | X | - | - | - | - | - | Backbone |
| 5-Aminoallyl-dU | - | X | - | DNA | CEP | Amino | - | - |
| 5'-Azido-dT | X | - | - | DNA | CEP | Click | CuAAC / SPAAC | - |
| 5-Br-dU | - | X | - | DNA | CEP | - | - | - |
| 5-Carboxy-dC (5cadC) | - | X | - | DNA | CEP | - | Epigenetic | - |
| 5-Ethynyl-dU (EdU) | - | X | - | DNA | CEP | Click | CuAAC | - |
| 5-Ethynyl-U (ErU) | - | X | - | RNA | CEP | Click | CuAAC | - |
| 5-Formyl-dC (5fdC / fdC) | - | X | - | DNA | CEP | - | Epigenetic | - |
| 5-Hydroxymethyl-dC (5hmdC / hmdC) | - | X | - | DNA | CEP | - | Epigenetic | - |
| 5'-Iodo-dT | X | - | - | DNA | CEP | - | - | - |
| 5-Methyl-dC (5mdC / mdC) | - | X | - | DNA | CEP | - | - | - |
| 5-Methyl-dZebularine | - | X | - | DNA | CEP | - | - | - |
| 5-TIPS-Ethynyl-dU (TIPS-EdU) | - | X | - | DNA | CEP | Click | CuAAC | - |
| 7-Deaza-dA | - | X | - | DNA | CEP | - | - | - |
| 7-Deaza-dG | - | X | - | DNA | CEP | - | - | - |
| 7-Deaza-G | - | X | - | RNA | CEP | - | - | - |
| 7-Ethynyl-7-Deaza-dA (EdA) | - | X | - | DNA | CEP | Click | CuAAC | - |
| 8-Azanebularine | - | X | - | RNA | CEP | - | - | - |
| 8-Oxo-dA | - | X | - | DNA | CEP | - | - | - |
| AbasicAlkyne | X | X | X | - | CEP | Click | CuAAC | - |
| Abberior### | X | - | X | - | NHS | Fluorophore | - | - |
| Abberior###-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Acrydite | X | - | X | - | NHS | - | - | - |
| Acrydite-dA/dC/dG/dT | - | X | - | DNA | NHS | - | - | - |
| AlexaFlour##-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| AlexaFluor### | X | - | X | - | NHS | Fluorophore | - | - |
| Amino(AbasicAmine) | X | X | X | - | CEP | Amino | - | - |
| Amino(C12) | X | - | - | - | CEP | Amino | - | - |
| Amino(C3) | X | - | - | - | CEP | Amino | - | - |
| Amino(C6) | X | - | X | - | CEP | Amino | - | - |
| Amino(C7) | X | X | X | - | CEP | Amino | - | - |
| Amino12 | X | - | - | - | CEP | Amino | - | - |
| Amino18 | X | - | - | - | CEP | Amino | - | - |
| Amino6 | X | - | - | - | CEP | Amino | - | - |
| Amino-C2-dT | - | X | - | DNA | CEP | Amino | - | - |
| Amino-C6-dA/dC/dG/dT | - | X | - | DNA | CEP | Amino | - | - |
| Amino-C6-U | - | X | - | RNA | CEP | Amino | - | - |
| Atto### | X | - | X | - | NHS | Fluorophore | - | - |
| Atto###-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Atto###LS | X | - | X | - | NHS | Fluorophore | - | Large-Stokes-Shift |
| Atto###LS-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | Large-Stokes-Shift |
| AttoMB2 (Methylene Blue) | X | - | X | - | NHS | Fluorophore | Redox | - |
| AttoMB2 (Methylene Blue)-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | Redox | - |
| Azide(C3) | X | - | X | - | NHS | Click | CuAAC / SPAAC | - |
| Azide(C3)-dA/dC/dG/dT | - | X | - | DNA | NHS | Click | CuAAC / SPAAC | - |
| Azide(PEG4) | X | - | X | - | NHS | Click | CuAAC / SPAAC | - |
| Azide(PEG4)-dA/dC/dG/dT | - | X | - | DNA | NHS | Click | CuAAC / SPAAC | - |
| Azobenzene | X | X | X | - | CEP | Quencher | - | - |
| BBQ650 | X | - | X | - | CEP | Quencher | - | - |
| BHQ0 | - | - | X | - | CEP | Quencher | - | - |
| BHQ1 | X | X | X | - | CEP | Quencher | - | - |
| BHQ1-dA/dC/dG/dT | - | X | - | DNA | NHS | Quencher | - | - |
| BHQ1-dT | - | X | - | DNA | CEP | Quencher | - | - |
| BHQ2 | X | X | X | - | CEP | Quencher | - | - |
| BHQ2-dA/dC/dG/dT | - | X | - | DNA | NHS | Quencher | - | - |
| BHQ2-dT | - | X | - | DNA | CEP | Quencher | - | - |
| BHQ3 | X | X | X | - | CEP | Quencher | - | - |
| BHQ3-dA/dC/dG/dT | - | X | - | DNA | CEP + Click | Quencher | - | - |
| Biotin(C3) | - | - | X | - | CEP | Biotin | - | - |
| Biotin(C6) | X | - | X | - | NHS | Biotin | - | - |
| Biotin(TEG) | X | - | X | - | CEP | Biotin | - | - |
| Biotin-dA/dC/dG/dT | - | X | - | DNA | NHS | Biotin | - | - |
| Bodipy### | X | - | X | - | NHS | Fluorophore | - | - |
| Bodipy###-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| C8-Alkyne-dA/dC/dU | - | X | - | DNA | CEP | Click | CuAAC | - |
| Carboxy(C10) | - | X | - | - | CEP | - | - | - |
| Carboxy(C6) | - | X | - | - | CEP | - | - | - |
| Carboxy-dT | - | X | - | DNA | CEP | - | - | - |
| CDPI3 | - | - | X | - | SP | - | Duplex Stabilizer | MGB |
| CDPI3-BHQ1 | - | - | X | - | SP | Quencher | Duplex Stabilizer | MGB |
| CDPI3-BHQ2 | - | - | X | - | SP | Quencher | Duplex Stabilizer | MGB |
| CFO560 | X | - | - | - | CEP | Fluorophore | - | - |
| CFO560-dT | - | X | - | DNA | CEP | Fluorophore | - | - |
| CFR590 | X | - | - | - | CEP | Fluorophore | - | - |
| CFR610 | X | - | - | - | CEP | Fluorophore | - | - |
| CFR610-dT | - | X | - | DNA | CEP | Fluorophore | - | - |
| Cholesterol | X | X | X | - | CEP | - | - | Transfection |
| Cholesterol(TEG) | X | X | X | - | CEP | - | - | Transfection |
| cnvK | - | X | - | - | CEP | - | - | - |
| Custom Wobble | - | X | - | DNA | CEP | - | Degeneration | SELEX |
| Custom Wobble (EdU(TIPS)) clickable | - | X | - | DNA | CEP | Click | CuAAC | Click SELEX |
| Custom Wobble (EdU) clickable | - | X | - | DNA | CEP | Click | CuAAC | Click SELEX |
| Custom Wobble (LNA) +M/R/W/S/Y/K/V/H/D/B/N | - | X | - | RNA | CEP | - | Duplex Stabilizer | Backbone |
| Custom Wobble (RNA) rM/R/W/S/Y/K/V/H/D/B/N | - | X | - | RNA | CEP | - | Degeneration | Backbone |
| Cy3 | X | X | X | - | NHS | Fluorophore | - | - |
| Cy3B | X | - | X | - | NHS | Fluorophore | - | - |
| Cy3B-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Cy3-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Cy5 | X | - | X | - | NHS | Fluorophore | - | - |
| Cy5.5 | X | - | X | - | NHS | Fluorophore | - | - |
| Cy5.5-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Cy5-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Cyan500 | X | - | X | - | NHS | Fluorophore | - | - |
| Cyan500-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| d5SICS | - | X | - | DNA | CEP | - | - | Synthetic Biology |
| DBCO(C2) | X | - | X | - | NHS | Click | SPAAC | - |
| DBCO(C2)-dA/dC/dG/dT | - | X | - | DNA | NHS | Click | SPAAC | - |
| DBCO(PEG4) | X | - | X | - | NHS | Click | SPAAC | - |
| DBCO(PEG4)-dA/dC/dG/dT | - | X | - | DNA | NHS | Click | SPAAC | - |
| DBCO(TEG) | X | - | X | - | CEP | Click | SPAAC | - |
| DBCO(TEG)-dT | - | X | - | DNA | CEP | Click | SPAAC | - |
| ddC | - | - | X | - | SP | - | Elongation Blocker | - |
| Desthiobiotin | X | - | X | - | NHS | Biotin | - | - |
| Desthiobiotin(TEG) | X | - | - | - | CEP | Biotin | - | - |
| Desthiobiotin-dA/dC/dG/dT | - | X | - | DNA | NHS | Biotin | - | - |
| Digoxigenin | X | - | X | - | NHS | - | - | Antigen |
| Digoxigenin-dA/dC/dG/dT | - | X | - | DNA | NHS | - | - | Antigen |
| Disulfide(C3) | X | - | X | - | NHS | Sulfide | - | - |
| Disulfide(C3)-dA/dC/dG/dT | - | X | - | DNA | NHS | Sulfide | - | - |
| Disulfide(C6) | X | X | X | - | CEP | Sulfide | - | Cleavable |
| dK | - | X | - | DNA | CEP | - | Degeneration | - |
| dNam | - | X | - | DNA | CEP | - | - | Synthetic Biology |
| dP | - | X | - | DNA | CEP | - | Degeneration | - |
| DTPA | X | X | X | - | CEP | Sulfide | - | - |
| dTPT3 | - | X | - | DNA | CEP | - | - | Synthetic Biology |
| DY-### | X | - | X | - | NHS | Fluorophore | - | - |
| DY-###-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| DY-###XL | X | - | X | - | NHS | Fluorophore | - | Large-Stokes-Shift |
| DY-###XL-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | Large-Stokes-Shift |
| FAM | X | - | X | - | NHS | Fluorophore | - | - |
| FAM-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Ferrocen | X | - | X | - | NHS | - | Redox | - |
| Ferrocen-dA/dC/dG/dT | - | X | - | DNA | NHS | - | Redox | - |
| HEX | X | - | X | - | NHS | Fluorophore | - | - |
| HEX-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Hexynyl | X | - | - | - | CEP | Click | CuAAC | - |
| Inosine(2'OMe-I) | - | X | - | RNA | CEP | - | Degeneration | - |
| Inosine(dI) | - | X | - | - | CEP | - | Degeneration | - |
| Inosine(rI) | - | X | - | RNA | CEP | - | Degeneration | - |
| IRD### | X | X | X | - | NHS | Fluorophore | - | - |
| IRD###-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| JOE | X | X | X | - | NHS | Fluorophore | - | - |
| JOE-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| LC610 | X | - | X | - | NHS | Fluorophore | - | - |
| LC610-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| LC640 | - | X | - | - | NHS | Fluorophore | - | - |
| LC640-dA/dC/dG/dT | X | - | X | DNA | NHS | Fluorophore | - | - |
| LC-Biotin | X | - | X | - | NHS | Biotin | - | - |
| LC-Biotin-dA/dC/dG/dT | - | X | - | DNA | NHS | Biotin | - | - |
| LC-LC-Biotin | X | X | X | - | NHS | Biotin | - | - |
| LC-LC-Biotin-dA/dC/dG/dT | - | X | - | DNA | NHS | Biotin | - | - |
| LNA-A/mC/G/T | - | X | - | RNA | CEP | - | Duplex Stabilizer | Backbone |
| Maleimid | X | - | - | - | CEP | - | - | - |
| Methylphosphonate-dA/dC/dG/dT | - | X | - | DNA | CEP | - | - | Backbone |
| Methyltetrazin | - | X | - | - | NHS | Click | IEDDA | - |
| Methyltetrazin(PEG4) | - | X | - | - | NHS | Click | IEDDA | - |
| Methyltetrazin(PEG4)-dA/dC/dG/dT | X | - | X | DNA | NHS | Click | IEDDA | - |
| Methyltetrazin-dA/dC/dG/dT | X | - | X | DNA | NHS | Click | IEDDA | - |
| MGB-Eclipse (MGB) | - | - | X | - | SP | Quencher | Duplex Stabilizer | MGB |
| N1-Methyl-PseudoUridine | - | X | - | RNA | CEP | - | - | - |
| N6-Methyl-A | - | X | - | RNA | CEP | - | Epigenetic | - |
| N6-Methyl-dA | - | X | - | DNA | CEP | - | Epigenetic | - |
| pdC | - | X | - | DNA | CEP | - | Duplex Stabilizer | - |
| pdU | - | X | - | DNA | CEP | - | Duplex Stabilizer | - |
| PEG10kDa | X | - | - | - | NHS | - | - | PEG |
| PEG20kDa | X | - | - | - | NHS | - | - | PEG |
| PEG5kDa | X | - | - | - | NHS | - | - | PEG |
| Peptide | X | - | X | - | Click | - | - | - |
| Phos | X | - | X | - | CEP | - | Elongation Blocker | - |
| PseudoUridine | - | X | - | RNA | CEP | - | - | - |
| Puromycin | - | - | X | - | SP | - | - | - |
| Pyrene | X | X | X | - | NHS | Fluorophore | - | - |
| Quasar670 | X | - | X | - | NHS | Fluorophore | - | - |
| Quasar670-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Quasar705 | X | - | - | - | CEP | Fluorophore | - | - |
| Quasar705-dT | - | X | - | DNA | CEP | Fluorophore | - | - |
| rA/rC/rG/rU | - | X | - | RNA | CEP | - | - | Backbone |
| rev-dA/dC/dG/dT | - | X | - | DNA | CEP | - | Elongation Blocker | Backbone |
| rev-LNA-A/mC/G/T | - | X | - | RNA | CEP | - | Duplex Stabilizer | Backbone |
| rev-rA/rC/rG/rU | - | X | - | RNA | CEP | - | - | Backbone |
| ROX | - | - | X | - | NHS | Fluorophore | - | - |
| ROX-dA/dC/dG/dT | X | - | - | DNA | NHS | Fluorophore | - | - |
| rTPT3 | - | X | - | RNA | CEP | - | - | Synthetic Biology |
| Spacer(C12) | X | X | X | - | CEP | Spacer | - | - |
| Spacer(C2) | X | X | X | - | CEP | Spacer | - | - |
| Spacer(C3) | X | X | X | - | CEP | Spacer | Elongation Blocker | - |
| Spacer(C6) | X | X | X | - | CEP | Spacer | - | - |
| Spacer(dSpacer) | X | X | X | - | CEP | Spacer | - | Backbone |
| Spacer(PC) | X | X | X | - | CEP | Spacer | - | Cleavable |
| Spacer(rev-dSpacer) | X | X | X | - | CEP | Spacer | Elongation Blocker | Backbone |
| Spacer(rSpacer) | X | X | X | - | CEP | Spacer | - | Backbone |
| Spacer18(HEG) | X | X | X | - | CEP | Spacer | - | PEG |
| Spacer9(TEG) | X | X | X | - | CEP | Spacer | - | PEG |
| TAMRA | X | - | X | - | NHS | Fluorophore | - | - |
| TAMRA-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| TCO | X | - | X | - | NHS | Click | IEDDA | - |
| TCO(PEG4) | X | - | X | - | NHS | Click | IEDDA | - |
| TCO(PEG4)-dA/dC/dG/dT | - | X | - | DNA | NHS | Click | IEDDA | - |
| TCO-dA/dC/dG/dT | - | X | - | DNA | NHS | Click | IEDDA | - |
| TexasRed | X | - | X | - | NHS | Fluorophore | - | - |
| TexasRed-dA/dC/dG/dT | - | X | - | DNA | NHS | Fluorophore | - | - |
| Thiol(C3) | X | - | X | - | NHS | Sulfide | - | - |
| Thiol(C3)-dA/dC/dG/dT | - | X | - | DNA | NHS | Sulfide | - | - |
| Thiol(C6) | X | - | X | - | CEP | Sulfide | - | - |
| TRIM Degeneration | - | X | - | DNA | CEP | - | Degeneration | - |
| Trimethoxystilbene Cap | X | - | - | - | CEP | - | - | Cap |
| Uridine(dU) | - | X | - | DNA | CEP | - | Epigenetic | - |
| YakimaYellow | X | - | - | - | CEP | Fluorophore | - | - |
| Zebularine | - | X | - | RNA | CEP | - | - | - |
Please contact us if you require a modification that is not included in our standard offerings.
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