Linkers

Phosphoramidite technology is ideally suited for the modification of synthetic oligonucleotides with covalently attached reporter moieties, linkers, spacers or haptens. Proligo provides popular reporters and linkers ready to use for DNA/RNA synthesis machines such as ß-cyanoethyl phosphoramidites.
Amino linkers can be employed to conjugate biotin, fluorescein or other modifiers and reporter groups to the 5′end of oligonucleotides, or to attach oligonucleotides to surfaces. Sigma-aldrich offers 2 monomethoxytrityl-protected amino linkers (MMT-linkers) and 2 trifluoroacetyl protected amino linkers (TFA linkers):

  • Trifluoroacetyl (TFA)-protected pentyl (C5) amino linker
  • Trifluoroacetyl (TFA)-protected hexyl (C6) amino linker
  • Monomethoxytrityl (MMT)-protected amino linker
  • ssH-linker: the next generation of MMT linker

Monomethoxytrityl (MMT)-protected amino linker
The MMT-group can be cleaved on the synthesis instrument with acidic deblock solution to enable on-support labeling protocols. Alternatively, the MMT-amino linker can be attached in the trityl-on mode of the instrument to provide purification handle similar to the DMT-group of the conventional oligonucleotides. The MMT-group is then removed with aqueous acid after purification with either RP-HPLC or a purification cartridge.

Trifluoroacetyl (TFA)-protected amino linker
The base-labile TFA-group is easily removed with concentrated ammonia during the cleavage and deprotection step. Additional deprotection steps are not necessary.

Key features of Amino Linkers
  • Completely soluble in acetonitrile
  • Proligo Reagents offers base-labile or acid-labile protecting groups on the amino linker, depending upon the application
  • Amino linker products are coupled with standard synthesis protocols, identical to the coupling pf DNA monomer phosphoramidites
  • No change in auxiliary synthesis reagents is required
  • The MMT-amino linker features a lipophilic group which aids in purification of the modified oligonucleotide after synthesis
  • The acid-labile MMT-group permits the colorimetric, determination of the coupling efficiency
  • It is recommended to deprotect MMT-amino linker oligonucleotides in concentrated ammonia at a lower temperature e.g. at 40°C for 24 hours
  • The MMT-group can be removed in aqueous solution with 80% acetic acid at room temperature for 24 hours
  • TFA-amino linker is completely deprotected with concentrated ammonia. Additional deprotection steps are not necessary

MMT-Linker Phosphoramidite

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M021030 MMT-Hexylaminolinker Phosphoramidite C35H48N3O3P configured for ABI
 
M021000 MMT-Hexylaminolinker Phosphoramidite C35H48N3O3P    
M021080 MMT-Hexylaminolinker Phosphoramidite C35H48N3O3P configured for PerkinElmer
configured for Polygen
 

ssH-Linker Phosphoramidite

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M024000 ssH-Linker C38H53N4O5P    
M024030 ssH-Linker C38H53N4O5P configured for ABI
 
M024080 ssH-Linker C38H53N4O5P configured for PerkinElmer
configured for Polygen
 

TFA-C5-Linker Phosphoramidite

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M022000 TFA-Pentylaminolinker Phosphoramidite C16H29F3N3O3P    
M022030 TFA-Pentylaminolinker Phosphoramidite C16H29F3N3O3P configured for ABI
 
M022080 TFA-Pentylaminolinker Phosphoramidite C16H29F3N3O3P configured for PerkinElmer
configured for Polygen
 

TFA-C6-Linker Phosphoramidite

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M023000 TFA-Hexylaminolinker Phosphoramidite C17H31F3N3O3P    
M023030 TFA-Hexylaminolinker Phosphoramidite C17H31F3N3O3P configured for ABI
 
M023080 TFA-Hexylaminolinker Phosphoramidite C17H31F3N3O3P configured for PerkinElmer
configured for Polygen