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Oligo Modifications

A wide variety of modifications can be incorporated into an oligonucleotide at the time of synthesis. When possible, this is done using a modified solid support (CPG) for 3'-modifications or a specialized phosphoramidite reagent for internal and 5'-modifications.

Design and Analysis tools

Related Products

CategoryModificationSequence CodeMolecular WeightAbmaxEmmax
Attachment Chemistry / Linkers5' 5-Octadiynyl dU/55OctdU/394.3  
 5' AcryditeTM/5Acryd/247.2  
 5' Adenylation/5rApp/410.2  
 5' Amino Modifier C12/5AmMC12/263.3  
 5' Amino Modifier C6/5AmMC6/179.2  
 5' Amino Modifier C6 dT/5AmMC6T/458.4  
 5' Azide (NHS Ester)/5AzideN/318.3  
 5' Biotin/5Biosg/393.4  
 5' Biotin (Azide)/5BioK/486.5  
 5' Biotin dT/5BiodT/684.7  
 5' Biotin-TEG/5BiotinTEG/481.5  
 5' Desthiobiotin-TEG/5deSBioTEG/539.6  
 5' Digoxigenin (NHS Ester)/5DigN/722.9  
 5' Dithiol/5DTPA/214.2  
 5' Dual Biotin/52-Bio/871  
 5' Hexynyl/5Hexynyl/160.1  
 5' I-Linker 1.2/5ILink12/208.2  
 5' PC Biotin/5PCBio/597.6  
 5' Thiol Modifier C6 S-S/5ThioMC6-D/328.4  
 5' Uni-LinkTM Amino Modifier/5UniAmM/209.2  
 3' 5-Octadiynyl dU/35OctdU/394.3  
 3' Amino Modifier/3AmMO/211.2  
 3' Amino Modifier C6 dT/3AmMC6T/458.4  
 3' Azide (NHS Ester)/3AzideN/350.3  
 3' Biotin/3Bio/437.4  
 3' Biotin dT/3BiodT/684.7  
 3' Biotin-TEG/3BioTEG/569.6  
 3' Cholesterol-TEG/3CholTEG/756  
 3' Desthiobiotin-TEG/3deSBioTEG/539.6  
 3' Digoxigenin (NHS Ester)/3Dig_N/754.9  
 3' Dithiol/3DTPA/214.2  
 3' Thiol Modifier C3 S-S/3ThioMC3-D/244.3  
 Int 5-Octadiynyl dU/i5OctdU/394.3  
 Int Amino Modifier C6 dT/iAmMC6T/458.4  
 Int Azide (NHS Ester)/iAzideN/597.6  
 Int Biotin (Azide)/iBiodUK/720.7  
 Int Biotin dT/iBiodT/684.7  
 Int Desthiobiotin-TEG/ideSBioTEG/539.6  
 Int Dithiol/iDTPA/214.2  
 Int Uni-LinkTM Amino Modifier/iUniAmM/209.2  
Dark Quenchers3' Black Hole Quencher® 1/3BHQ_1/554.5534 
 3' Black Hole Quencher® 2/3BHQ_2/556.5578 
 3' Dabcyl/3Dab/757.8478 
Fluorophores5' 5-TAMRATM (Azide)/55-TAMK/673.7546579
 5' 6-FAMTM/56-FAM/537.5495520
 5' 6-FAMTM (Azide)/56-FAMK/618.5496516
 5' 6-FAMTM (NHS Ester)/56-FAMN/537.5496516
 5' Alexa Fluor® 488 (NHS Ester)/5Alex488N/695.6492517
 5' Alexa Fluor® 532 (NHS Ester)/5Alex532N/787.8527553
 5' Alexa Fluor® 546 (NHS Ester)/5Alex546N/1121.5555571
 5' Alexa Fluor® 594 (NHS Ester)/5Alex594N/883.9584616
 5' Alexa Fluor® 647 (NHS Ester)/5Alex647N/1020.2650670
 5' Alexa Fluor® 660 (NHS Ester)/5Alex660N/941.7661691
 5' Alexa Fluor® 750 (NHS Ester)/5Alex750N/1047.2753775
 5' ATTOTM 488 (NHS Ester)/5ATTO488N/750.2502522
 5' ATTOTM 532 (NHS Ester)/5ATTO532N/807.8534554
 5' ATTOTM 550 (NHS Ester)/5ATTO550N/755.2560575
 5' ATTOTM 565 (NHS Ester)/5ATTO565N/672.7570591
 5' ATTOTM 590 (NHS Ester)/5ATTO590N/752.9602624
 5' ATTOTM 633 (NHS Ester)/5ATTO633N/713.2635653
 5' ATTOTM 647N (NHS Ester)/5ATTO647NN/807.2649662
 5' ATTOTM Rho101 (NHS Ester)/5RHO101N/751.2592609
 5' Cy3TM/5Cy3/506.6550564
 5' Cy5.5TM/5Cy55/632.7685706
 5' Cy5TM/5Cy5/532.6648668
 5' Dy 750 (NHS Ester)/5Dy750N/875.1747776
 5' Fluorescein dT/5FluorT/816.7495520
 5' HEXTM /5HEX/744.1538555
 5' IRDye® 700/5IRD700/753.9684702
 5' IRDye® 800/5IRD800/862.1791809
 5' JOE (NHS Ester)/56-JOEN/666.4529555
 5' LightCycler 640 (NHS Ester)/5LtC640N/902.9620635
 5' MAXTM (NHS Ester)/5MAXN/619.7524557
 5' Rhodamine GreenTM -X (NHS Ester)/5RhoG-XN/648.7504531
 5' RhodamineRedTM -X (NHS Ester)/5RhoR-XN/833574594
 5' ROXTM (NHS Ester)/56-ROXN/695.8588608
 5' TAMRATM (NHS Ester)/56-TAMN/591.6559583
 5' TETTM /5TET/675.2522539
 5' TEX 615/5TEX615/966.1596613
 5' Texas Red®-X (NHS Ester)/5TexRd-XN/881598617
 5' TYETM563/5TYE563/490.6549563
 5' TYETM665/5TYE665/516.6645665
 5' WellREDTM D2/5D2/640.8763778
 5' WellREDTM D3/5D3/644.8683701
 5' WellREDTM D4/5D4/544.7648666
 5’ IRDye 800CW (NHS Ester)/5IRD800CWN/1163.3767791
 3' 6-FAMTM/36-FAM/569.5495520
 3' 6-FAMTM (NHS Ester)/3FAM_N/569.5496516
 3' Alexa Fluor® 488 (NHS Ester)/3AlexF488N/727.6492517
 3' Alexa Fluor® 532 (NHS Ester)/3AlexF532N/819.8527553
 3' Alexa Fluor® 546 (NHS Ester)/3AlexF546N/1153.5555571
 3' Alexa Fluor® 594 (NHS Ester)/3AlexF594N/915.9584616
 3' Alexa Fluor® 647 (NHS Ester)/3AlexF647N/1052.2650670
 3' Alexa Fluor® 660 (NHS Ester)/3AlexF660N/973.7661691
 3' Alexa Fluor® 750 (NHS Ester)/3AlexF750N/1079.2753775
 3' ATTOTM 488 (NHS Ester)/3ATTO488N/782.2502522
 3' ATTOTM 532 (NHS Ester)/3ATTO532N/839.2534554
 3' ATTOTM 550 (NHS Ester)/3ATTO550N/787.2560575
 3' ATTOTM 565 (NHS Ester)/3ATTO565N/704.7570591
 3' ATTOTM 590 (NHS Ester)/3ATTO590N/784.9602624
 3' ATTOTM 633 (NHS Ester)/3ATTO633N/745.2635653
 3' ATTOTM 647N (NHS Ester)/3ATTO647NN/839.2649662
 3' ATTOTM Rho101 (NHS Ester)/3RHO101N/783.2592609
 3' Cy3TM-Sp/3Cy3Sp/644.6550564
 3' Cy5.5TM-Sp/3Cy55Sp/770.8685706
 3' Cy5TM-Sp/3Cy5Sp/670.7648668
 3' Fluorescein dT/3FluorT/816.7495520
 3' LightCycler® 640 (NHS Ester)/3LtCy640N/934.9620635
 3' Rhodamine GreenTM -X (NHS Ester)/3RhodGn-XN/680.7504531
 3' RhodamineRedTM -X (NHS Ester)/3RhodRd-XN/865574594
 3' TAMRA (NHS Ester)-Sp/36-TAMTSp/1008.9559583
 3' TAMRATM-Sp/36-TAMSp/1008.9559583
 3' TEX 615/3TEX615/897596613
 3' Texas Red®-X (NHS Ester)/3TxRed-XN/913598617
 3' TYE™ 563/3TYE563/634.8550565
 3' TYE™ 665/3TYE665/774648666
 Int 5-TAMRATM (Azide)/i5-TAMK/907.9546579
 Int 6-FAMTM (Azide)/i6-FAMK/852.8496516
 Int Cy3TM/iCy3/506.6550564
 Int Cy5TM/iCy5/532.6648668
 Int Fluorescein dT/iFluorT/816.7495520
 Int TAMRATM (NHS Ester)/i6-TAMN/870.9559583
Iowa Black® Dark Quenchers5' Iowa Black® FQ/5IABkFQ/442.4531 
 5' Iowa Black® RQ/5IAbRQ/420.4656 
 3' Iowa Black® FQ/3IABkFQ/442.4531 
 3' Iowa Black® RQ-Sp/3IAbRQSp/678.6667 
Modified Bases5' 2'-Fluoro A/52FA/331.2  
 5' 2'-Fluoro C/52FC/307.2  
 5' 2'-Fluoro G/52FG/347.2  
 5' 2'-Fluoro U/52FU/308.2  
 5' 2, 6-Diaminopurine/5AmdA/328.2278 
 5' 2-Aminopurine/52AmPr/313.2303371
 5' 5-Bromo dU/55Br-dU/369.1278 
 5' 5-Hydroxymethyl dC/55HydMe-dC/319.2  
 5' 5-Methyl dC/5Me-dC/303.2277 
 5' 5-Nitroindole/55NitInd/340.2265 
 5' deoxyInosine/5deoxyI/314.2  
 5' deoxyUridine/5deoxyU/290.2  
 5' Inverted Dideoxy-T/5InvddT/288.2  
 5' isodC/5Me-isodC/303.2  
 5' isodG/5isodG/329.2  
 3' 2'-Fluoro A/32FA/331.2  
 3' 2'-Fluoro C/32FC/307.2  
 3' 2'-Fluoro G/32FG/347.2  
 3' 2'-Fluoro U/32FU/308.2  
 3' 2, 6-Diaminopurine/3AmdA/328.2278 
 3' 2-Aminopurine/32AmPu/313.2303371
 3' 5-Hydroxymethyl dC/35HydMe-dC/319.2  
 3' 5-Me dC/3Me-dC/303.2  
 3' 5-Nitroindole/35NitInd/340.2265 
 3' deoxyInosine/3deoxyI/314.2  
 3' deoxyUridine/3deoxyU/290.2  
 3' Dideoxy-C/3ddC/273.2  
 3' Inverted dT/3InvdT/304.2  
 Int 2'-Fluoro A/i2FA/331.2  
 Int 2'-Fluoro C/i2FC/307.2  
 Int 2'-Fluoro G/i2FG/347.2  
 Int 2'-Fluoro U/i2FU/308.2  
 Int 2, 6-Diaminopurine/i6diPr/328.2278 
 Int 2-Aminopurine/i2AmPr/313.2303371
 Int 5-Bromo dU/i5Br-dU/369.1278 
 Int 5-Hydroxymethyl dC/i5HydMe-dC/319.2  
 Int 5-Methyl dC/iMe-dC/303.2277 
 Int 5-Nitroindole/i5NitInd/340.2265 
 Int deoxyInosine/ideoxyI/314.2  
 Int deoxyUridine/ideoxyU/290.2  
 Int isodC/iMe-isodC/303.2  
 Int isodG/iisodG/329.2  
Phosphorylation5' Phosphorylation/5Phos/80  
 3' Phosphorylation/3Phos/80  
Spacers5' C3 Spacer/5SpC3/138.1  
 5' dSpacer/5dSp/180.1  
 5' PC Spacer/5SpPC/344.3  
 5' Spacer 18/5Sp18/344.3  
 5' Spacer 9/5Sp9/212.1  
 3' C3 Spacer/3SpC3/138.1  
 3' dSpacer/3dSp/180.1  
 3' Hexanediol/3C6/180.1  
 3' Spacer 18/3Sp18/344.3  
 3' Spacer 9/3Sp9/212.1  
 Int C3 Spacer/iSpC3/138.1  
 Int dSpacer/idSp/180.1  
 Int PC Spacer/iSpPC/344.3  
 Int Spacer 18/iSp18/344.3  
 Int Spacer 9/iSp9/212.1