Designed for oligonucleotide synthesis for diagnostic and therapeutic development

Linker phosphoramidites provide options to link oligonucleotides to additional groups (e.g., chemical delivery system for therapeutics, fluorescent dyes, amines, phosphates) or attach to a solid surface like a DNA chip. On the other hand, spacer phosphoramidites can alter oligonucleotide conformation and/or reduce steric hinderance for applications such as aptamers and tagging/labeling assays.

Our linker phosphoramidite offerings include monomethoxytrityl (MMT) or trifluoroacetic acid (TFA) protection, for addition of a primary amine to the 5′ position of oligonucleotides. Phosphorylation phosphoramidites are also available for incorporation of phosphate group to the 5′ or 3′ position of oligonucleotides, for increased stability and ligation applications.

Our spacer phosphoramidite offerings include three carbons (C3), spacer 18 (HEG), and reverse abasic.

Our linker and spacer phosphoramidites are supported by:

  • Technical expertise—over 40 years of partnership, customization, and scale-up experience
  • Secure and consistent supply—5x capacity expansion in 2022 to support emerging therapeutics and diagnostic assays
  • Service excellence—48 hours or less response to orders, >98% delivery to customer at promised date†
  • Flexible packaging—custom and bulk packaging available upon request
  • Refined quality—ISO 9001:2015–certified quality management system that has been refined in partnership with our customers since 1995

† May not be applicable in all regions.

Quality manufacturing and documentation

Processes are monitored from material procurement through final QC and product release for batch-to-batch reproducibility. Purity of each phosphoramidite lot may be assessed by HPLC, NMR, and water determination by the Karl Fischer method. Our rigorously controlled manufacturing processes help minimize levels of reactive impurities which could be incorporated into the oligonucleotide during synthesis and result in the accumulation of by-products.

Linkers, 5′-amino linkers, and phosphorylating CEPs

Thermo Scientific 5′ amino linker ß-cyanoethyl phosphoramidites (CEP) are available as MMT or TFA protected.

  • The MMT protection allows for trityl-on purification of the resulting oligonucleotide and is suitable for purification by reverse-phase techniques.
  • The base-labile TFA group works for 5′-amino modification when oligo purification is not necessary before conjugation. The TFA group is removed during ammonia deprotection.

Thermo Scientific phosphorylating CEP can be 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 a solid support.

 5′-Aminohexyl Linker CEPTFA-Aminolinker CEPPhosphorylating CEP
Cat. No.27-003527-179227-1794
Chemical name6-(4-monomethoxytritylamino)-hexyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite6-(N-trifluoroacetylamino)hexyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite2-[2-(4,4-dimethoxytrityloxy)ethylsulfonyl]ethyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Molecular weight589.75 g/mol413.42 g/mol656.66 g/mol
CAS #114616-27-2133975-85-6108783-02-4
HPLC purity≥97%NA≥95%
31P NMR purityNA≥90.0%NA
Shipping conditionDry iceDry iceAmbient, desiccated. Keep vial upright during storage
Water contentNA≤0.3%NA
Storage condition–20°C

Ordering information

For quotes, flexible/bulk packaging, custom services, or items not listed above, please contact us or submit your inquiry.

Spacer modifiers

The Thermo Scientific C3 spacer CEP can be used to incorporate a three-carbon spacer or add sequentially to create longer spacer arms. Thermo Scientific spacer 18 hexaethyleneglycol (HEG) CEP reduces possible steric hinderance effects and/or protection from exonucleases. Thermo Scientific reverse abasic CEP introduces abasic sites in oligonucleotides to study their biological effects.

 C3-Spacer-CEPHEG (Spacer 18) phosphoramiditeReverse abasic CEP
Cat. No.27-179527-178627-1998
Chemical name3-(4,4'-dimethoxytrityloxy)propyl-1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite18-O-(4,4'-dimethoxytrityl)-Hexaethyleneglycol-1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite3-O-(4,4’-dimethoxytrityl)-1,4-anhydro-2-deoxy-D-ribitol-5-O-(β-cyanoethyl-N,N-diisopropyl)
Molecular weight578.7 g/mol784.9 g/mol620.72 g/mol
HPLC purity≥98%≥95%≥98%
31P NMR purity≥98%≥98%≥98%
Material sourceNon animal source (no TSE/BSE risk)
Shipping / storage conditionDry ice / –20°C

Ordering information

For quotes, flexible/bulk packaging, custom services, or items not listed above, please contact us or submit your inquiry.

For Research Use Only. Not for use in diagnostic procedures.