Linker and Spacer Phosphoramidites

The addition of primary amine groups to oligonucleotides are utilized to attach a variety of modifiers (eg. NHS ester fluors) or the attachment to a solid surface. Choose from either 5′-Aminohexyl Linker or TFA-amino linker to add a primary amine to the 5' position of your oligonucleotide sequence.  Or for the addition of a phosphate to the 5' position, choose phosphorylating amidite.  All three can be found below in the Linkers drop down menu. Spacer phosphoramidites can be utilized to change the oligonucleotide conformation and/or reduce steric hinderance for applications such as aptamers and tagging/labeling assays.

Linker and spacer phosphoramidites by synthesizer compatibility

Linkers and 5'-modifiers

The addition of primary amino groups to oligonucleotides are utilized to attach a variety of modifiers (eg. Biotin, fluorescent dye, etc.) or attachment to a solid surface. Thermo Scientific amino linkers, TFA and MMT phosphoramidites are used for the addition of a primary amine to the 5′ position of an oligonucleotide.  Phosphorylating Phosphoramidites are used for addition of a phosphate group to the 5′ position of an oligonucleotide (final synthesis addition), or 3′-end when used as the first addition off of any solid support.

  • The 5′ amino modifier amidites are supplied with MMT (27-0035) or TFA (27-1792) protection
  • The MMT modifier allows for trityl-on purification of the resulting oligonucleotide and is a suitable choice when wanting to purify by reverse phase techniques.
  • The base-labile TFA group is a good choice for 5′-amino modification when oligo purification isn’t necessary, prior to conjugation. The TFA group is removed during ammonia deprotection.
  • Oligos with an amino modification can also be attached to surfaces in DNA chip applications.

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  5′-Aminohexyl Linker CEP TFA-Aminolinker CEP Phosphorylating
Cat. No. 27-0035 27-1792 27-1794
Chemical name 6-(4-Monomethoxytritylamino)-hexyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite 6-(N-Trifluoroacetylamino)hexyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite 2-[2-(4,4-Dimethoxytrityloxy)ethylsulfonyl]ethyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Formula C35H48N3O3P C17H31F3N3O3P C34H45F3N2O7PS
Molecular weight 589.75 g/mol 413.42 g/mol 656.66 g/mol
CAS # 114616-27-2 133975-85-6 108783-02-4
HPLC purity ≥ 97.0% NA ≥ 95.0%
31P NMR purity NA ≥ 90.0% NA
Shipping condition Dry ice Dry ice Ambient, desiccated. Keep vial upright during storage
Water content NA ≤ 0.3% NA
Storage condition –20 °C –20 °C
–20 °C
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–20 °C
–20 °C
–20 °C

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Spacer Modifiers

  • Utilize C3 spacer amidite to incorporate a three carbon spacer or add sequentially to create longer spacer arms.
  • Select C18 HEG amidite to reduce possible steric hinderance effects and/or protection from exonucleases.
  • An abasic oligo can be formed using the dSpacer amidite.

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  dSpacer-CEP C3-Spacer-CEP HEG (Spacer 18) phosphoramidite
Cat. No. 27-1768 27-1795 27-1786
Chemical name 5′-O-(4,4'-Dimethoxytrityl)-1',2'-dideoxyribose-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite 3-(4,4'-Dimethoxytrityloxy)propyl-1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite 18-O-(4,4'-Dimethoxytrityl)-Hexaethyleneglycol-1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Formula C35H45N2O6P
Molecular weight 602.7 g/mol 578.7 g/mol 784.9 g/mol
CAS # 129821-76-7 NA NA
Hazardous No
HPLC purity ≥ 95% ≥ 98.0% ≥ 95.0%
31P NMR purity ≥ 95% ≥ 98.0% ≥ 98%
Material Source non-animal source (no TSE/BSE risk)
Shipping / Storage  condition Dry ice / –20 °C
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Process and supply chain control

  • Processes are monitored from material procurement through final QC and product release, providing batch-to-batch reproducibility
  • A controlled raw material supply chain and established vendor partnerships ensure consistency and security of supply
  • Purity of each spacer-modified phosphoramidite lot is assessed by HPLC and 31P NMR analyses
  • Rigorously controlled manufacturing processes minimize levels of reactive P(III) impurities which could be incorporated into the oligonucleotide and result in the accumulation of by-products

Flexible packaging

  • Common oligo synthesizer pack sizes are available for immediate delivery
  • Custom and bulk packaging are also available. Contact us to learn more.

Custom services

  • Custom manufacturing services are available to assist in the development or scale-up of phosphoramidite compounds
  • Specialty phosphoramidites can be manufactured with base or sugar (2′, 3′ or 5′ positions) modifications


Not finding what you are looking for? We also offer DNA phosphoramiditesRNA phosphoramiditesspecialty phosphoramiditesdye-labeled phosphoramidites2′-modifications, and succinates and CPG support synthesis supportsContact us to learn more.