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.

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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 reversed-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.

Availability by compatible synthesizer compatibility

 Linker phosphoramidites
 5′-Aminohexyl Linker CEPTFA-AminolinkerPhosphorylating CEP
Applied Biosystems/AKTA SynthesizerCustom orders available for 27-0035.
Request quote		27-1792
Request quote		27-1794-04
Expedite Synthesizer27-1794-09
MerMade Synthesizer27-1794-10

Technical specifications for linker phosphoramidites

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 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
FormulaC35H48N3O3PC17H31F3N3O3PC34H45N2O7PS
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

Compatibility by synthesizer model

Linker phosphoramidites are compatible with the following oligonucleotide synthesizers:

  • Applied Biosystems / AKTA Synthesizer
  • Expedite Synthesizer
  • MerMade Synthesizer

Applied Biosystems and AKTA synthesizer

Compatible catalog product is ready-to-ship in amber bottles with serum vial neck style.

Expedite synthesizer

Available catalog SKU is supplied in 30 mL amber bottle with a 20-400 finish neck style.

MerMade systems synthesizer

Order catalog product ready-to-ship in a 30 mL amber bottle with a 28-400 finish neck style.

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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 helps reduce possible steric hinderance effects and/or protection from exonucleases. Thermo Scientific reverse abasic CEP introduces abasic sites in oligonucleotides to study their biological effects.

Availability by compatible synthesizer compatibility

 Spacer phosphoramidites
 C3-Spacer-CEPHEG (Spacer 18) phosphoramiditeReverse abasic CEP
Applied Biosystems/AKTA Synthesizer27-1795-0427-1786-0227-1998

Request quote
Expedite Synthesizer
MerMade Synthesizer27-1795
Request quote		27-1786
Request quote

Technical specifications of spacer phosphoramidites

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 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)
FormulaC33H43N2O5PC42H61N2O10PC35H45N2O6P
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

Compatibility by synthesizer model

Spacer phosphoramidites are compatible with the following oligonucleotide synthesizers:

Applied Biosystems and AKTA synthesizer

Compatible catalog product is ready-to-ship in amber bottles with serum vial neck style.

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Resources

Phosphoramidite Learning Resource

Access webinars, videos, articles, and more to optimize your success in oligonucleotide synthesis for diagnostic and therapeutic manufacturing process development.

mRNA Production Learning Library

Browse the educational assets related to raw materials selection, process development using in vitro transcription, scale-up synthesis, and the latest trends in mRNA production.

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

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