Universal Linker "PT Linker Support"
The Phenanthrene-type Linker (PT Linker) is a universal linker for oligonucleotide synthesis. This linker consists of a bicyclic 1,2-diol structure containing a phenanthrene moiety and a succinyl unit that connects the solid support to the phenanthrene via an amide bond. Its high lipophilicity and UV-detectable phenanthrene scaffold facilitate easy separation of the targeted oligonucleotide from linker-derived impurities. 1)
Structure of PT Linker
Highly lipophilic and UV-detectable
phenanthrene scaffold
Features
- Easy detection and separation of the targeted product from PT-derived components
- Usable under the same reaction conditions as conventional universal linkers
- Prevents ring-opening reactions typical of maleimide (MI)-type universal linkers
Mechanism of Oligonucleotide Cleavage from the Universal Support
Comparison of Universal Supports
Type of Universal Supports
Phenanthrene-type (PT) Linker
Maleimide-type (MI) Linker
Expected Products Derived from the PT Linker under Base Treatment Condition
(Oligonucleotides with attached linker)
Products Derived from MI-type Linkers under Base Treatment Condition
| Closed ring products |  |
 |
 |
 |
| Open ring products |  |
 |
 |
 |
| oligonucleotide-PT (Oligonucleotides with attached linker) |
p-MI | cp-MI | MI |
|---|
Oligonucleotide Synthesis in DMTr-off Mode
Figure 2 HPLC analysis of ONs released from T10-loaded (a) MI Linker CPG (R=Me) and (b)(c) PT Linker CPG after treatment with 28% NH3 (aq.) at rt for 2 h. HPLC analytical conditions: (a) 5-15% (b) 8-18% (c) 5-50% Acetonitrile in 0.1 M TEAA (pH 7.0) over a linear gradient for 30 min.
Applications
Synthesis of Oligonucleotide (T10) in DMTr-off Mode
Figure 3 HPLC analysis of ONs released from T10-loaded PT Linker CPG under Basic conditions A and B. Basic condition A: (a),(b) 28% NH3 (aq.) at 55℃ for 8 h; Basic condition B: (c) AMA at 65℃ for 1 h. HPLC analytical conditions: (a),(c) 8-18% (b) 5-50% Acetonitrile in 0.1 M TEAA (pH 7.0) over a linear gradient for 30 min.
Synthesis of Oligonucleotides containing Various Nucleoside at the 3'-Terminus (DMTr-off Mode)
Figure 4 HPLC analysis of ONs released from CPG 1-5 after treatment with 28% NH3 (aq.) at 55℃ for 8 h. HPLC analytical conditions: 8-18% Acetonitrile in 0.1 M TEAA (pH 7.0) over a linear gradient for 30 min.
Synthesis of Oligonucleotide (s-oligo) in DMTr-off Mode
Figure 5 HPLC analysis of ONs released from s-oligo-loaded (a) MI Linker CPG (R=Me) and (b)(c) PT Linker CPG under Basic conditions A and B. Basic condition A: (a),(b) 28% NH3 (aq.) at 55℃ for 3 h; Basic condition B: (c) 28% NH3 (aq.) at 55℃ for 8 h. HPLC analytical conditions: 5-25% Acetonitrile in 0.1 M TEAA (pH 7.0) over a linear gradient for 30 min.
Synthesis of 12-mer Oligonucleotides Containing All Four Nucleotides in DMTr-off Mode
Figure 6 HPLC analysis of ONs released from oligo-loaded PT Linker CPG under Basic conditions (a) 28% NH3 (aq.) at 55℃ for 8 h and (b) 20% Diethylamine (DEA) in Acetonitrile at rt for 10 min then 28% NH3 (aq.) at 55℃ for 8 h. HPLC analytical conditions: 8-18% Acetonitrile in 0.1 M TEAA (pH 7.0) over a linear gradient for 30 min.
References
- Fuchi, Y., Yamamoto, K., Ito, Y. and Hari, Y. : Synthesis, 55, 1112 (2023).
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