RNA Modifiers
Technical Note11/17/2019 2:11 pm

Published on November 17, 2019

While most modifications to RNA are built for maintenance, demand in new and improved compounds is growing for various use of synthetic RNA. A major one is gRNA for recent CRISPR/CAS9 systems, but the more veteran application for RNA modifiers is undoubtedly antisense RNA. In order to harness the mechanistic advantages of RNA interference,  custom nucleotide sequences need to be equipped with the ability to permeate cell walls, bind to the target and protect itself from degradation. We offer an advanced selection of 2’-O-alkyl/methyl compounds along with affinity and fluorescent labels to follow a sequence in experiments all throughout its development.

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

RNA Synthesis/Modifiers & Labelling

N 3 -Methyl-uridine-DMTr-3'-Icaa CPG 
N 3 -Thiobenzoylethyl-uridine-DMTr-3'-Icaa CPG 
N 4 -Ethyl-cytidine-DMTr-3'-Icaa CPG 
N 6 -Benzyl-adenosine-DMTr-3'-Icaa CPG 
N 6 -Isopentenyl-adenosine-DMTr-3'-Icaa CPG 
Pseudo-uridine-DMTr-3'-Icaa CPG 
Purine-riboside-DMTr-3'-Icaa CPG 
Thymidine-DMTr-3'-Icaa CPG 
Uridine-DMTr-3'-Icaa CPG 
β -L- Thymidine-DMTr-3'-Icaa CPG 
β -L-Adenosine ( N -Bz)-DMTr 3'-Icaa CPG 
β -L-Cytidine ( N -Ac)-DMTr 3'-Icaa CPG 
β -L-Cytidine ( N -Bz)-DMTr 3'-Icaa CPG 
β -L-Guanosine ( N -iBu)-DMTr 3'-Icaa CPG 
β -L-Uridine-DMTr 3'-Icaa CPG 
(2)-Amino (TFA) Protected RNA 3'-CPG 
2-Amino-2'-amino (TFA)-uridine-DMTr-3'-Icaa CPG 
2'-Amino (TFA)-cytidine ( N -Bz) CPG 
Puromycin Supports 
3'-L- O -Methyl-tyrosine-puromycin-2'- Icaa CPG 
Puromycin 2'-succinyl Icaa CPG 
RNA Synthesis: Purification Kit 
Anhydrous Ammonia in Ethanol Solution (20% ammonia by wt in absolute ethanol) 
Fluoride Ion Removal Solution 
Tetra butyl Ammonium Fluoride (1 M Sol in THF) 
Levulinyl Deprotection Solution 
Levulinyl Deprotection Solution 
O-Alkyl & Antisenses Oligonucleotide Modifications

2'- O -Methyl-RNA Synthesis 

A: CE Phosphoramidites (RNA synthesis)
(1)-2'-O-Me RNA Phosphoramidites 
2'- O -Methyl-adenosine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl-adenosine ( N -Bz)-MMTr-3'-CEP 
2'- O -Methyl-cytidine ( N -Ac)-DMTr-3'-CEP 
2'- O -Methyl-cytidine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Methyl-guanosine ( N -iBu)-MMTr-3'-CEP 
2'- O -Methyl-uridine-DMTr-3'-CEP 
(2)-2'-O-Me RNA Phosphoramidites (mild protection) 
2'- O -Methyl-adenosine ( N -PAC)-DMTr-3'-CEP 
2'- O -Methyl-cytidine ( N -Ac)-DMTr-3'-CEP 
2'- O -Methyl-cytidine ( N -PAC)-DMTr-3'-CEP 
2'- O -Methyl-guanosine ( N -DMF)-DMTr-3'-CEP 
2'- O -Methyl-guanosine ( N -iPrPAC)-DMTr-3'-CEP 
2'- O -Methyl-guanosine ( N -PAC)-DMTr-3'-CEP 
2'- O -Methyl-uridine-DMTr-3'-CEP 
B: Minor 2'-O-Me-RNA Phosphoramidites 
2'- O -Methyl-5-propynyl-uridine-DMTr-3'-CEP 
2'- O -Methyl-uridine (C-6)-DMTr-3'-CEP (Amino Modifier)\" 
2'- O -Methyl-2,6-diamino-purine ( N 2, N 6-diPAC)-DMTr-3'-CEP 
2'- O -Methyl-4-triazolyl-uridine-DMTr-3'-CEP 
2'- O -Methyl-5-bromo-uridine-DMTr-3'-CEP 
2'- O -Methyl-5-iodo-uridine-DMTr-3'-CEP 
2'- O -Methyl-5-methyl-cytidine ( N -Ac)-DMTr-3'-CEP 
2'- O -Methyl-5-methyl-cytidine ( N -Bz)-DMTr-3'-CEP 
2'-O-Methyl-5-methyl-cytidine ( N -DMF)-DMTr-3'-CEP 
2'- O -Methyl-5-methyl-uridine (Ribo Thymidine)-DMTr-3'-CEP 
2'- O -Methyl-5-propynyl-cytidine ( N -Bz)-DMTr-3'-CE 
2'- O -Methyl-7-deaza 7-iodo-adenosine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl-7-deaza 7-Iodo-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Methyl-7-deaza-7-propargyl (Amino- TFA)-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Methyl-7-deaza-7-propargyl(Amino-TFA)-adenosine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl-7-deaza-adenosine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl-7-deaza-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Methyl-cytidine ( N -DMF)-DMTr-3'-CEP (Amino Modifier) 
2'- O -Methyl-Inosine-DMTr-3'-CEP 
C-Backbone 2'-O-Me-RNA modificatios 
(1)- P-O -Ethyl Phosphoramidites 
2'- O -Methyl- P-O -ethyl-adenosine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl- P-O -ethyl-adenosine ( N -PAC)-DMTr-3'-CEP 
2'- O -Methyl- P-O -ethyl-cytidine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl- P-O -ethyl-cytidine ( N -PAC)-DMTr-3'-CEP 
2'- O -Methyl- P-O -ethyl-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Methyl- P-O -ethyl-guanosine ( N -PAC)-DMTr-3'-CEP 
2'- O -Methyl- P-O- ethyl-thymidine-DMTr-3'-CEP 
2'- O -Methyl- P-O- ethyl-uridine-DMTr-3'-CEP 
(2)-Methyl RNA Phosphoramidites 
2'- O -Methyl- P -methyl-adenosine ( N -Bz)-DMTr-3'-CEP 
2'- O -Methyl- P -methyl-cytidine ( N -Ac)-DMTr-3'-CEP 
2'- O -Methyl- P -methyl-cytidine ( N -iBu)-DMTr-3'-CEP 
2'- O -Methyl- P -methyl-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Methyl- P -methyl-uridine-DMTr-3'-CEP 
D: Supports For 2'-OME RNA Synthesis 
(1)-2'-OMe-RNA 3'-CPG 
2'- O -Methyl-adenosine ( N -Bz)-DMTr-3'-Icaa CPG 
2'- O -Methyl-cytidine ( N -Ac)-DMTr-3'-Icaa CPG 
2'- O -Methyl-cytidine ( N -Bz)-DMTr-3'-Icaa CPG 
2'- O -Methyl-guanosine ( N -DMF)-MMTr-3'-Icaa CPG 
2'- O -Methyl-guanosine ( N -iBu)-DMTr-3'-Icaa CPG 
2'- O -Methyl-uridine-DMTr-3'-Icaa CPG 
(2)-2'-OMe-RNA 3'-CPG (mild protection) 
2'- O -Methyl-adenosine ( N -PAC)-DMTr-3'-Icaa CPG 
2'- O -Methyl-cytidine ( N -Ac)-DMTr-3'-Icaa CPG 
2'- O -Methyl-cytidine ( N -PAC)-DMTr-3'-Icaa CPG 
2'- O -Methyl-guanosine ( N -PAC)-DMTr-3'-Icaa CPG 
(3)-Minor 2'-OMe-RNA 3'-CPG  
2'- O -Methyl-5-methyl-cytidine ( N -DMF)-DMTr-3'-Icaa CPG 
2'- O -Methyl-5-bromo-uridine-DMTr-3'-Icaa CPG 
2'- O -Methyl-5-iodo-uridine-DMTr-3'-Icaa CPG 
2'- O -Methyl-5-methyl-cytidine ( N -Bz)-DMTr-3'-Icaa CPG 
2'- O -Methyl-inosine-DMTr-3'-Icaa CPG 
2'- O -Methyl-thymidine-DMTr-3'-Icaa CPG

2'-O-Me 5'→ 3' RNA Synthesis 

A: 2'-O-Me 5'-CE RNA Phosphoramidites 
2'- O -Methyl-adenosine ( N -Bz)-DMTr-5'-CEP 
2'- O -Methyl 5-methyl-uridine-DMTr-5'-CEP 
2'- O -Methyl-5-methyl-cytidine ( N -Bz)-DMTr-5'-CEP 
2'- O -Methyl-cytidine ( N -Ac)-DMTr-5'-CEP 
2'- O -Methyl-cytidine ( N -Bz)-DMTr-5'-CEP 
2'- O -Methyl-guanosine ( N -iBu)-DMTr-5'-CEP 
2'- O -Methyl-uridine-DMTr-5'-CEP 
B: Support:2'-O-Me 5'-CPG 
2'- O -Methyl-5-methyl-cytidine ( N -Bz)-DMTr-5'-Icaa CPG 
2'- O -Methyl-5-methyl-uridine-DMTr-5'-Icaa CPG 
2'- O -Methyl-adenosine ( N -Bz)-DMTr-5'-Icaa CPG 
2'- O -Methyl-cytidine ( N -Ac)-DMTr-5'-Icaa CPG 
2'- O -Methyl-cytidine ( N -Bz)-DMTr-5'-Icaa CPG 
2'- O -Methyl-guanosine ( N -iBu)-DMTr-5'-Icaa CPG 
2'- O -Methyl-uridine-DMTr-5'-Icaa CPG

2'-F RNA Synthesis 

A: CE Phosphoramidites 
(1)-2'-F-RNA Monomers 
2'-Fluoro-2'-deoxyadenosine ( N -DMF)-DMTr-3'-CEP 
2'-Fluoro-2'-deoxyadenosine ( N -Bz)-DMTr-3'-CEP 
2'-Fluoro-2'-deoxycytidine ( N -Ac)-DMTr-3'-CEP 
2'-Fluoro-2'-deoxyguanosine ( N -DMF)-DMTr-3'-CEP 
2'-Fluoro-2'-deoxyguanosine ( N -iBu)-DMTr-3'-CEP 
2'-Fluoro-2'-deoxyuridine-DMTr-3'-CEP 
(2)-2'-F-RNA Monomers (Ultramild) 
2'-Fluoro-2'-deoxyadenosine ( N -PAC)-DMTr-3'-CEP 
2'-Fluoro-2'-deoxycytidine ( N -Ac)-DMTr-5'-CEP 
2'-Fluoro-2'-deoxyguanosine ( N -iPrPAC)-DMTr-3'-CEP 
2'-Fluoro-2'-deoxyuridine-DMTr-5'-CEP 
B: Minor 2'-F-RNA Monomers 
2'-Fluoro-2'-deoxyinosine-DMTr-3'-CEP 
2'-Fluoro-5-iodo-2'-deoxyuridine-DMTr-3'-CEP 
2'-Fluoro-5-methyl-2'-deoxycytidine ( N -Ac)-DMTr-3'-CEP 
2'-Fluoro-5-methyl-2'-deoxycytidine ( N -Bz)-DMTr-3'-CEP 
2'-Fluoro-5-methyl-2'-deoxyuridine-DMTr-3'-CEP 
C: Supports  
(1)-Support-3'-CPG 
2'-Fluoro-2'-deoxyadenosine ( N -DMF)-DMTr-3'-Icaa CPG 
2'-Fluoro-2'-deoxyadenosine ( N -Bz)-DMTr-3'-Icaa CPG 
2'-Fluoro-2'-deoxycytidine ( N -Ac)-DMTr-3'-Icaa CPG 
2'-Fluoro-2'-deoxyguanosine ( N -DMF)-DMTr-3'-Icaa CPG 
2'-Fluoro-2'-deoxyguanosine ( N -iBu)-DMTr-3'-Icaa CPG 
2'-Fluoro-2'-deoxyuridine-DMTr-3'-Icaa CPG

2'- O -Butyne RNA Synthesis 

A: 2'-O-Butyne-RNA Phosphonamidites 
2'- O -Butyne-aenosine ( N -Bz)-DMTr 3'-CEP 
2'- O -Butyne-cytidine ( N -Bz)-DMTr-3'-CEP 
2'- O -Butyne-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Butyne-uridine-DMTr-3'-CEP 
B: Supports: 2'-O-Butyne-RNA 3'-CPG 
2'- O -Butyne-adenosine ( N -Bz)-DMTr-3'-Icaa CPG 
2'- O -Butyne-cytidine ( N -Bz)-DMTr-3'-Icaa CPG 
2'- O -Butyne-guanosine ( N -iBu)-DMTr-3'-Icaa CPG 
2'- O -Butyne-uridine-DMTr-3'-Icaa CPG

RNA: 2'- O -Propargyl RNA Synthesis (Combiclick TM  Chemistry) 

A: 2'- O -Propargyl RNA Phosphoramidites  
2'- O -Propargyl-adenosine ( N -Bz)-DMTr-3'-CEP 
2'- O -Propargyl-cytidine ( N -Ac)-DMTr-3'-CEP 
2'- O -Propargyl-cytidine ( N -Bz)-DMTr-3'-CEP 
2'- O -Propargyl-guanosine ( N -iBu)-DMTr-3'-CEP 
2'- O -Propargyl-inosine-DMTr-3'-CEP 
2'- O -Propargyl-uridine-DMTr-3'-CEP 
B: 2'-O-Propargyl RNA:Minor Phosphoramidites 
2'- O -Propargyl-abasic-DMTr-3’-CEP; 2'- O -Propargyl-1,1 dihydro-β-D-ribose-DMTr-3’-CEP 
2'- O -Propargyl-abasic-DMTr-3’-Icaa CPG 
Ara-Propargyl-inosine-DMTr-3’-CEP 
C: Supports-2'-O-Propargyl RNA 3'-CPG 
2'- O -Propargyl-adenosine ( N -Bz) DMTr 3'-Icaa CPG 
2'- O -Propargyl-cytidine ( N -Ac) DMTr 3'-Icaa CPG 
2'- O -Propargyl-cytidine ( N -Bz) DMTr 3'-Icaa CPG 
2'- O -Propargyl-guanosine ( N -iBu) DMTr 3'-Icaa CPG 
2'- O -Propargyl-inosine DMTr 3'-Icaa CPG 
2'- O -Propargyl-uridine  DMTr 3'-Icaa CPG

RNA: 2'-O-Hexyne RNA Synthesis 

A: 2'-O-Hexyne RNA Phosphoramidites 
2'- O -Hexyne-inosine-DMTr-3’-CEP 
2'- O -Hexyne-1,1 dihydro-β-D-ribose-DMTr-3’-CEP

RNA: 3'-O-Alkyl RNA Synthesis 

A: 3'- O -Alkyl RNA phosphoramidites 
(1)-3'- O -Methyl-RNA Phosphoramidites  
3'- O -Methyl-adenosine ( N -Bz)-DMTr-2'-CEP 
3'- O -Methyl-cytidine ( N -Ac)-DMTr-2'-CEP 
3'- O -Methyl-cytidine ( N -Bz)-DMTr-2'-CEP 
3'- O -Methyl-guanosine ( N -iBu)-DMTr-2'-CEP 
3'- O -Methyl-inosine-DMTr-2'-CEP 
3'- O -Methyl-thymidine-DMTr-2'-CEP 
3'- O -Methyl-uridine-DMTr-2'-CEP 
(2)-3'-O-Propargyl RNA Phosphoramidites 
3'- O -Propargy-cytidine ( N -Ac)-DMTr-2'-CEP 
3'- O -Propargyl-adenosine ( N -Bz)-DMTr-2'-CEP 
3'- O -Propargyl-cytidine ( N -Bz)-DMTr-2'-CEP 
3'- O -Propargyl-guanosine ( N -iBu)-DMTr-2'-CEP 
3'- O -Propargyl-uridine-DMTr-2'-CEP 
B: 3'-O-Alkyl RNA Supports 
(1)-Supports:3'- O -ME-RNA 2'-CPG  
3'- O -Methyl-adenosine ( N -Bz)-DMTr-2'-Icaa CPG 
3'- O -Methyl-cytidine ( N -Bz)-DMTr-2'-Icaa CPG 
3'- O -Methyl-guanosine ( N -iBu)-DMTr-2'-Icaa CPG 
3'- O -Methyl-inosine-DMTr-2'-Icaa CPG 
3'- O -Methyl-uridine-DMTr-2'-Icaa CPG 
(2)-Supports:3'-O-Propargyl RNA 2'-CPG 
3'- O -Propargyl-adenosine ( N -Bz)-DMTr-2'-Icaa CPG 
3'- O -Propargyl-cytidine ( N -Ac)-DMTr-2'-Icaa CPG 
3'- O -Propargyl-cytidine ( N -Bz)-DMTr-2'-Icaa CPG 
3'- O -Propargyl-guanosine ( N -iBu)-DMTr-2'-Icaa CPG 
3'- O -Propargyl-uridine-DMTr-2'-Icaa CPG