5-aminohexyl linker phosphoramidite
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.
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 CEP | TFA-Aminolinker | Phosphorylating CEP | |
| Applied Biosystems/AKTA Synthesizer | Custom orders available for 27-0035. Request quote | 27-1792 Request quote | 27-1794-04 |
| Expedite Synthesizer | 27-1794-09 | ||
| MerMade Synthesizer | 27-1794-10 | ||
Technical specifications for linker phosphoramidites
Click images to enlarge
TFA-aminolinker phosphoramidite
Phosphorylating phosphoramidite
| 5′-Aminohexyl Linker CEP | TFA-Aminolinker CEP | Phosphorylating CEP | |
|---|---|---|---|
| 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% | NA | ≥95% |
| 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 | ||
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.
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-CEP | HEG (Spacer 18) phosphoramidite | Reverse abasic CEP | |
| Applied Biosystems/AKTA Synthesizer | 27-1795-04 | 27-1786-02 | 27-1998 Request quote |
| Expedite Synthesizer | |||
| MerMade Synthesizer | 27-1795 Request quote | 27-1786 Request quote | |
Technical specifications of spacer phosphoramidites
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C3-spacer-CEP
HEG (spacer 18) phosphoramidite
Reverse abasic CEP
| C3-Spacer-CEP | HEG (Spacer 18) phosphoramidite | Reverse abasic CEP | |
|---|---|---|---|
| Cat. No. | 27-1795 | 27-1786 | 27-1998 |
| Chemical name | 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 | 3-O-(4,4’-dimethoxytrityl)-1,4-anhydro-2-deoxy-D-ribitol-5-O-(β-cyanoethyl-N,N-diisopropyl) |
| Formula | C33H43N2O5P | C42H61N2O10P | C35H45N2O6P |
| Molecular weight | 578.7 g/mol | 784.9 g/mol | 620.72 g/mol |
| HPLC purity | ≥98% | ≥95% | ≥98% |
| 31P NMR purity | ≥98% | ≥98% | ≥98% |
| Material source | Non animal source (no TSE/BSE risk) | ||
| Shipping / storage condition | Dry ice / –20°C | ||
Compatibility by synthesizer model
Spacer phosphoramidites are compatible with the following oligonucleotide synthesizers:
- Applied Biosystems / AKTA Synthesizer
- Expedite Synthesizer: Custom order only; contact us for a quote
- MerMade Synthesizer: Custom order only; contact us for a quote
Applied Biosystems and AKTA synthesizer
Compatible catalog product is ready-to-ship in amber bottles with serum vial neck style.
Looking for additional size options, customization, or packaging solutions?
For Research Use Only. Not for use in diagnostic procedures.
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