Compounds for RNA Synthesis
Technical Note11/17/2019 2:11 pm

The synthesis of RNA is conventionally more sensitive than DNA. This poses challenges in developing very similar synthesis compounds such as amidites and supports, but with the right chemistry to counter RNA-specific hurdles. Stability and structural confirmation are routine offenders, and both can be countered by utilizing backbone phosphorothioation and reverse synthesis techniques. β-L-RNA-Spiegelmers and minor RNA phosphoramidites offer novel solutions to end-user specificity. While TOM-amidites are highly suitable for large scale therapeutic grade RNA synthesis, long RNA sequences, aptamers, and biologically significant RNA molecules.

 

See the full list of in-house RNA Compounds used in our synthesis below:

 

RNA Synthesis

A: CE Phosphoramidites: TBDMS Protected 
(1)-TBDMS Protected 
Adenosine ( N -Ac)-DMTr-3'-CEP 
Adenosine ( N -Bz)-DMTr-3'-CEP 
Adenosine (N-Bz)-MMTr-3'-CEP 
Cytidine ( N -Ac)-DMTr-3'-CEP 
Cytidine ( N -Bz)-DMTr-3'-CEP 
Cytidine ( N -Bz)-MMTr-3'-CEP 
Guanosine ( N -Ac)-DMTr-3'-CEP 
Guanosine ( N -DMF)-DMTr-3'-CEP 
Guanosine ( N -iBu)-DMTr-3'-CEP 
Guanosine ( N -iBu)-MMTr-3'-CEP 
Uridine-DMTr-3'-CEP 
Uridine-MMTr-3'-CEP 
(2)-TBDMS Protected (Ultramild  base protection) 
Adenosine ( N -PAC)-DMTr-3'-CEP 
Adenosine ( N -PAC)-MMTr-3'-CEP 
Cytidine ( N -Ac)-DMTr-3'-CEP 
Cytidine ( N -PAC)-DMTr-3'-CEP 
Cytidine ( N -tBPAC)-MMTr-3'-CEP 
Guanosine ( N -iprPAC)-DMTr-3'-CEP  
Guanosine ( N -PAC)-DMTr-3'-CEP 
Guanosine ( N -PAC)-MMTr-3'-CEP 
Guanosine ( N -Phenyl-Ac)-DMTr-3'-CEP 
(3)-TOM Protected 
2'-TOM-Adenosine ( N -Ac)-DMTr-3'-CEP 
2'-TOM-Cytidine ( N -Ac)-DMTr-3'-CEP 
2'-TOM-Guanosine ( N -Ac)-DMTr-3'-CEP  
2'-TOM-Uridine-DMTr-3'-CEP 
(4)-Acetal levulinyl ester Protected 
2'-ALE-Adenosine ( N -PAc)-5'-NPPOC-3'-CEP 
2'-ALE-Cytidine ( N -iBu)-5'-NPPOC-3'-CEP 
2'-ALE-Guanosine ( N -PAc)-5'-NPPOC-3'-CEP 
2'-ALE-Uridine-5'-NPPOC-3'-CEP 
(5)-Pivaloyloxymethyl Protected 
2'-Pivom-Adenosine ( N -PAc)-DMTr-3'-CEP 
2'-Pivom-Cytidine ( N -Ac)-DMTr-3'-CEP 
2'-Pivom-Guanosine ( N -iPrPAC)-DMTr-3'-CEP 
2'-Pivom-Uridine-DMTr-3'-CEP 
B: Supports 
(1)-TBDMS Protected 3'-CPG 
Adenosine ( N -Bz)-DMTr-3'-Icaa CPG 
Cytidine ( N -Ac)-DMTr-3'-Icaa CPG  
Cytidine ( N -Bz)-DMTr-3'-Icaa CPG  
Guanosine ( N -iBu)-DMTr-3'-Icaa CPG 
Uridine-DMTr-3'-Icaa CPG 
(2)-TBDMS protected 3'-CPG (Ultramild  base protection)  
Adenosine ( N -PAC)-DMTr-3'-Icaa CPG 
Adenosine ( N -tBPAC)-DMTr- 3'-Icaa CPG 
Cytidine ( N -PAC)-DMTr-3'-Icaa CPG 
Guanosine ( N -PAC)-DMTr-3'-Icaa CPG 
Guanosine ( N -tBPAC)-DMTr-3'-Icaa CPG 
Uridine-DMTr-3'-Icaa CPG 
(3)-TBDMS protected 3'-Oxalyl CPG 
Adenosine ( N -PAC)-DMTr-3'-oxalyl Icaa-CPG 
Ammonia Free Oligo Deprotection Solution 
Cytidine ( N -PAC)-DMTr-3'-oxalyl  Icaa CPG 
Guanosine ( N -iBu)-DMTr-3'-oxalyl Icaa CPG 
Guanosine ( N -PAC)-DMTr-3'-oxalyl Icaa CPG 
Uridine-DMTr-3'-oxalyl Icaa CPG 
(4)-TBDMS protected 3'-Polystyrene 
Adenosine ( N -Bz)-DMTr-3'-succinyl Polystyrene 
Cytidine ( N -Ac)-DMTr-3'-succinyl Polystyrene 
Cytidine ( N -Bz)-DMTr-3'-succinyl Polystyrene 
Guanosine ( N -iBu)-DMTr-3'-succinyl Polystyrene 
Uridine-DMTr-3'-succinyl Polystyrene 
(5)-TBDMS protected-3'-Non-clevable long chain spacer 
2'-TBDMS Guanosine ( N -iBu)-DMTr-3'-non-clevable long chain space 
(6)-TOM protected 3'-CPG 
2'-TOM-Adenosine ( N -Ac)-DMTr-3'-Icaa CPG 
2'-TOM-Cytidine ( N -Ac)-DMTr-3'-Icaa CPG 
2'-TOM-Guanosine ( N -Ac)-DMTr-3'-Icaa CPG 
2'-TOM-Uridine-DMTr-3'-Icaa CPG 
B: Backbone modification:Methyl Phosphoramidite 
P-O -Methyl-adenosine ( N -Bz)-DMTr-3'-CEP 
P-O -Methyl-adenosine ( N -Bz)-MMTr-3'-CEP 
P-O -Methyl-adenosine ( N -PAC)-DMTr-3'-CEP 
P-O -Methyl-adenosine ( N -PAC)-MMTr-3'-CEP 
P-O -Methyl-cytidine ( N -Bz)-DMTr-3'-CEP 
P-O -Methyl-cytidine ( N -PAC)-DMTr-3'-CEP 
P-O -Methyl-guanosine ( N -iBu)-DMTr-3'-CEP 
P-O -Methyl-guanosine ( N -iBu)-MMTr-3'-CEP 
P-O -Methyl-guanosine ( N -PAC)-DMTr-3'-CEP 
P-O-Methyl-guanosine ( N -PAC)-MMTr-3'-CEP  
P-O -Methyl-uridine-DMTr-3'-CEP 

 

RNA: 5'→ 3' Synthesis 

A: CE Phosphoramidites: TBDMS Protected 
Adenosine ( N -Bz)-DMTr-5'-CEP 
Cytidine ( N -Ac)-DMTr-5'-CEP 
Cytidine ( N -Bz)-DMTr-5'-CEP 
Guanosine ( N -iBu)-DMTr-5'-CEP 
Guanosine ( N -iprPAC)-DMTr-5'-CEP  
Uridine-DMTr-5'-CEP 
B: Supports-TBDMS protected 5'-CPG 
Adenosine ( N -Bz)-DMTr-5'-Icaa CPG 
Cytidine ( N -Ac)-DMTr-5'-Icaa CPG  
Cytidine ( N -Bz)-DMTr-5'-Icaa CPG  
Guanosine ( N -iBu)-DMTr-5'-Icaa CPG 
Uridine-DMTr-5'-Icaa CPG 

 

Minor RNA Bases 

A: Minor RNA Phosphoramidites 
(1)-TBDMS Protected RNA Phosphoramidites 
2,2'-Anhydro-uridine-DMTr-3'-CEP 
2-Amino-adenosine-DMTr-3'-CEP, (2,6-Diamino Purine DMTr-3'-CEP) 
2-Amino-purine ( N -DMF)-DMTr-3'-CEP 
2-Amino-purine ( N -iBu)-DMTr-3'-CEP 
2-One-pyridine-DMTr-3'-CEP; Zebularine CEP 
4-Triazolyl-uridine-DMTr-3'-CEP 
4-Thio-uridine-DMTr-3'-CEP 
2-Thio-uridine-DMTr-3'-CEP 
5-Bromo-cytidine ( N -Bz)-DMTr-3'-CEP  
5-Bromo-uridine-DMTr-3'-CEP 
5-Fluoro-2'-deoxyuridine-DMTr-3'-CEP  
5-Iodo-cytidine ( N -Bz)-DMTr-3'-CEP 
5-Iodo-uridine-DMTr-3'-CEP 
5-Methyl-cytidine ( N -Bz)-DMTr-3'-CEP 
8-Bromo-adenosine ( N -DBF)-DMTr-3'-CEP 
8-Bromo-adenosine ( N -DMF)-DMTr-3'-CEP 
8-Bromo-guanosine ( N -DMF)-DMTr-3'-CEP 
8-methyl-guanosine ( N -iBu)-DMTr-3'-CEP 
8-Oxo-7-allyl-guanosine ( N -iBu)-DMTr-3'-CEP 
8-Oxo-guanosine ( N -DMF)-DMTr-3'-CEP 
Inosine-DMTr-3'-CEP 
N 3 -Methyl-thymidine-DMTr-3'-CEP  
N 3 -Methyl-uridine-DMTr-3'-CEP 
N 3 -Thiobenzoylethyl-uridine-DMTr-3'-CEP 
N 6 ,  N 6 -Dimethyl-adenosine-5'-DMTr-3'-CEP 
N 6 -Benzyl-adenosine-DMTr-3'-CEP 
N 6 -isopentenyl-adenosine-DMTr-3'-CEP  
N 4 -Ethyl-cytidine-DMTr-3'-CEP 
Purine-riboside-DMTr-3'-CEP; Nebularine CEP 
Thymidine-DMTr-3'-CEP 
5,6-Dihydro-uridine-DMTr-3'-CEP 
7-Deaza-7-cyano-adenosine ( N -Bz)-DMTr-3'-CEP 
7-Deaza-adenosine ( N -Bz)-DMTr-3'-CEP; Tubercidin 
7-Deaza-guanosine ( N -Ac)-DMTr-3'-CEP 
7-Deaza-guanosine ( N -iBu)-DMTr-3'-CEP 
7-Deaza-guanosine ( N -iBu)-DMTr-5'-CEP 
Iso-cytidine ( N -DBF)-DMTr-3'-CEP  
Iso-guanosine ( N -DBF)-DMTr-3'-CEP 
Adenosine ( N -Bz)-DMTr-2'-CEP 
Cytidine ( N -Ac)-DMTr-2'-CEP 
Cytidine ( N -Bz)-DMTr-2'-CEP 
Guanosine ( N -iBu)-DMTr-2'-CEP 
Inosine-DMTr-2'-CEP 
Uridine-DMTr-2'-CEP 
P-O -Ethyl-adenosine ( N -PAC)-DMTr-3'-CEP 
P-O -Ethyl-cytidine ( N -PAC)-DMTr-3'-CEP 
P-O -Ethyl-guanosine ( N -PAC)-DMTr-3'-CEP 
P-O -Ethyl-uridine-DMTr-3'-CEP 
Pseudo-uridine-DMTr-3'-CEP 
β-L-RNA-Spiegelmers
β -L-Adenosine ( N -Bz)-DMTr-3'-CEP 
β -L-Cytidine ( N -Ac)-DMTr-3'-CEP  
β -L-Cytidine ( N -Bz)-DMTr-3'-CEP  
β -L-Guanosine ( N -iBu)-DMTr-3'-CEP  
β -L-Thymidine-DMTr-3'-CEP 
β -L-Uridine-DMTr-3'-CEP 
(2)Amino TFA Protected RNA Phosphoramidites 
2'-Amino(TFA)-cytidine ( N -Bz)-DMTr-3'-CEP 
2-Amino-2'-Amino (TFA)-uridine-DMTr-3'-CEP 
5'-Amino (TFA)-cytidine ( N -Ac)-3'-CEP 
(3)-Acetyl Protected RNA Phosphoramidites 
2',3'-Diacetyl-guanosine ( N -iBu)-5'-CEP 
2',3'-Diacetyl-uridine-5'-CEP 
B: Supports-Minor-RNA-TBDMS Protected 3'-CPG 
(1)-TBDMS Protected RNA 3'-CPG 
2,2'-Anhydro-uridine-DMTr-3'-Icaa CPG 
2-Amino-adenosine-DMTr-3'-Icaa CPG  
2-Amino-purine-DMTr-3'-Icaa CPG 
2-One-pyridine-DMTr-3'-Icaa CPG; Zebularine CPG 
5-Bromo-cytidine ( N -Bz)-DMTr-3'-Icaa CPG 
5-Bromo-uridine-DMTr-3'-Icaa CPG 
5-Fluoro-uridine-DMTr-3'-Icaa CPG 
5-Iodo-cytidine ( N -Bz)-DMTr-3'-Icaa CPG 
5-Iodo-uridine-DMTr-3'-Icaa CPG 
5-Methyl-cytidine ( N -Bz)-DMTr-3'-Icaa CPG 
7-Deaza-adenosine ( N -Bz)-DMTr-3'-Icaa CPG; Tubercidin CPG 
7-Deaza-guanosine ( N -iBu)-DMTr-3'-Icaa CPG 
8-Bromo-adenosine ( N -DBF)-DMTr-3'-Icaa CPG 
8-Methyl-guanosine ( N -iBu)-DMTr-3'-Icaa CPG 
Adenosine ( N -Ac)-DMTr-3'-Icaa CPG 
Adenosine ( N -Bz)-DMTr-3'-Icaa CPG 
Cytidine ( N -Ac)-DMTr-3'-Icaa CPG  
Cytidine ( N -Bz)-DMTr-3'-Icaa CPG  
Guanosine ( N -iBu)-DMTr-3'-Icaa CPG 
Inosine-DMTr-3'-Icaa CPG 
Iso-Cytidine  ( N -DBF)-DMTr-3'-Icaa CPG 
Iso-Guanosine ( N -DBF)-DMTr-3'-Icaa CPG 
N 3 -Methyl-thymidine-DMTr-3'-Icaa CPG