Nucleosides & Amidites
Technical Note11/17/2019 2:11 pm

Published November 17, 2019

Often referred to as the building blocks of DNA & RNA, a nucleoside is essentially a ribose or deoxyribose sugar carrying a base (adenine, guanine, thymine, cytosine, or uracil) at it’s 1’ position. This complex plays a defining role in the production of quality oligonucleotide sequences. Synthetic versions of nucleosides called amidites are chemical compounds are available in various structures to support principals in sold phase synthesis-such as 5’ protection, directional confirmation, and coupling consistency. With the addition of an open phosphate group at the 3’, phosphoramidites introduce the most complete synthetic compound to simply plug into a custom synthesis design. 

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

Nucleosides: Unprotected mononucleosides

I-Unprotected deoxy mononucleosides 
A: Deoxy Nucleosides 
2'- β- D - Deoxyadenosine Monohydrate 
2'- β- D - Deoxycytidine (Free Base) 
2'- β- D - Deoxycytidine Monohydrate 
2'- β- D - Deoxyguanosine Monohydrate 
2'- β- D - Deoxyinosine 
2'- β- D - Deoxyuridine 
Thymidine Monohydrate 
B: Dideoxy nucleosides 
2',3'- β- D - Dideoxyadenosine 
2',3'- β- D - Dideoxycytidine 
2',3'- β- D - Dideoxyguanosine 
2',3'- β- D - Dideoxyinosine 
2',3'- β- D - Dideoxyuridine 
3'- β- D - Deoxythymidine 
C: Alpha deoxy nucleosides 
Alpha-D-2'-deoxyadenosine 
Alpha-D-2'-deoxycytidine 
Alpha-D-2'-deoxyguanosine 
Alpha-D-thymidine 
D: L-deoxy nucleosides 
2-Amino- β -L-2'-deoxyadenosine 
β -L-2'-deoxycytidine 
β -L-2'-deoxydenosine 
β -L-2'-deoxyguanosine 
β -L-2'-deoxyuridine 
β -L-thymidine 
E: 7-deaza deoxy Nucleosides 
7-Deaza-2'-deoxyadenosine 
7-Deaza-2'-deoxyguanosine 
7-Deaza-2'-deoxyInosine 
F:  N -Alkylated Nucleosides 
N 1 -Methyl-2'-deoxyadenosine 
N 1 -Methyl-2'-deoxyguanosine 
N 3 -Methyl-2'-deoxycytidine 
N 3 -Methyl-2'-deoxyuridine 
N 3 -Methyl-thymidine 
N 4 -Ethyl-2'-deoxycytidine 
N 4 -Methyl-2'-deoxycytidine 
N 6 -Methyl-2'-deoxyadenosine 
G: Halogenated Nucleosides 
5-Bromo-2'-deoxyuridine 
5-Bromo-2'-deoxycytidine 
5-Iodo-2'-deoxycytidine 
5-Iodo-2'-deoxyuridine 
7-Iodo-7-deaza-2'-deoxyadenosine 
7-Iodo-7-deaza-2'-deoxyguanosine 
8-Bromo-2'-deoxyadenosine 
8-Bromo-2'-deoxyguanosine 
H: Etheno Nucleosides 
Etheno-2'-deoxyadenosine 
Etheno-2'-deoxycytidine 
I: Thio Nucleosides 
4-Thio-2'-deoxyuridine 
4-Thio-thymidine 
6-Thio-2'-deoxyguanosine 
J: 5-Alkyl Nucleosides 
5-Methyl-2'-deoxycytidine 
5-Propynyl-2'-deoxycytidine 
5-Propynyl-2'-deoxyuridine 
K: Modified Base Nucleosides 
2'-Deoxynebularine; 2’-deoxy purine riboside 
5-Aza-2'-deoxycytidine; 4-Amino-1-(2-deoxy-ß-D-ribofuranosyl)-1,3,5-triazin-2(1H)-one 
L: Halogenated and deaza halogenated dideoxy Nucleosides 
5-Iodo 2',3'-dideoxycytidine 
5-Iodo-2',3'-dideoxyuridine 
7-Deaza-2',3'-dideoxyadenosine 
7-Deaza-2',3'-dideoxyguanosine 
7-Iodo-7-deaza-2',3'-dideoxyadenosine 
7-Iodo-7-deaza-2',3'-dideoxyguanosine 
M: 8-Oxo &  O 6  substituted Guanosine 
7-Deaza-O 6 -methyl-2'-deoxyguanosine 
8-Oxo-2'-deoxyguanosine 
O 6 -(Carboxymethyl)-2'-deoxyguanosine (Calcium Salt) 
N: 3'-Levulinyl Nucleoside 
3'-Levulinyl-2'-deoxyguanosine 
O: 2'-Amino Nucleoside 
2'-Amino-2'-deoxycytidine 
P: Azido deoxy Nucleoside 
3'-Azido-3’-deoxythymidine; Zidovudine; Retrovir

Nucleosides: II-Unprotected ribo mononucleosides

A: Ribo Nucleosides
Adenosine 
Cytidine 
Guanosine 
Inosine 
Ribothymidine,  5-Methyl-ribouridine 
Uridine 
B: 2'-Fluoro deoxy nucleosides
2'-Fluoro-2'-deoxyadenosine 
2'-Fluoro-2'-deoxycytidine 
2'-Fluoro-2'-deoxyguanosine 
2'-Fluoro-2'-deoxyuridine 
C: L-ribo nucleosides
β -L-Adenosine 
β -L-Cytidine 
β -L-Guanosine 
β -L-Inosine 
β -L-Thymidine 
β -L-Uridine 
D: 7-Deaza ribo Nucleosides 
7-Deaza-adenosine (Tubercidin) 
7-Deaza-guanosine 
7-Deaza-inosine 
E: 2'- O -Methyl ribo nucleosides 
2'- O -Methyl-adenosine 
2'- O -Methyl-cytidine 
2'- O -Methyl-guanosine 
2'- O -Methyl-inosine 
2'- O -Methyl-thymidine 
2'- O -Methyl-uridine 
F: 2'- O -Allyl ribo Nucleosides 
2'- O -Allyl-adenosine 
2'- O -Allyl-cytidine 
2'- O -Allyl-guanosine 
2'- O -Allyl-uridine 
G: 2'- O -Propargyl ribo Nucleosides 
2'- O -Propargyl-adenosine 
2'- O -Propargyl-cytidine 
2'- O -Propargyl-guanosine 
2'- O -Propargyl-uridine 
H: 3'- O -Methyl ribo Nucleosides 
3'- O -Methyl-5-methyl-cytidine 
3'- O -Methyl-adenosine 
3'- O -Methyl-cytidine 
3'- O -Methyl-guanosine 
3'- O -Methyl-inosine 
3'- O -Methyl-uridine 
I: 3'- O -Allyl ribo Nucleosides 
3'- O -Allyl-adenosine 
3'- O -Allyl-cytidine 
3'- O -Allyl-guanosine 
3'- O -Allyl-uridine 
J: 3'- O -Propargyl ribo Nucleosides 
3'- O -Propargyl-adenosine 
3'- O -Propargyl-cytidine 
3'- O -Propargyl-guanosine 
3'- O -Propargyl-uridine 
K: 5',3'-Tetraisopropyl disiloxane ribo Nucleoside 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Aadenosine 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Cytidine 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Guanosine 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Uridine 
L: Modified Base ribo Nucleosides 
2,6-Diamino-Purine-riboside 
2-Amino-Purine-riboside 
M: 2,2’-Anhydro ribo Nucleosides 
2,2'- O -Anhydro-5-methyl-cytidine 
2,2'- O- Anhydro-cytidine (HCl Salt), (Beta-D- O -2,2’-Cyclocytidine Ancitabine) 
2,2'- O- Anhydro-uridine (HCl Salt), (Beta-D- O -2,2’-Cyclouridine) 
N: Etheno ribo  nucleosides 
Etheno-adenosine 
Etheno-cytidine 
O:  N -alkylated ribo  nucleosides 
N 3 -Methyl-cytidine 
N 3 -Methyl-uridine 
N 6 -Dimethyl-adenosine 
N 6 -Palmitoy-adenosine 
P: 5-Alkyl ribo  nucleosides 
5-Methyl-cytidine 
5-Propynyl-cytidine 
5-Propynyl-uridine 
Q: Sustituted Ara Nucleosides 
Ara-5-methyl-cytidine 
Ara-7-deaza-guanosine 
Uridine-arabinose 
R: Thio Ribo Nucleosides 
4'-Thio-uridine 
8-Thio-guanosine 
S: Halogenated ribo nucleosides 
6-Chloro-inosine; 6-Chloropurine-riboside 
5-Bromo-cytidine 
5-Bromo-uridine 
5-Iodo-cytidine 
5-Iodo-uridine 
7-Iodo-7-deaza-adenosine 
8-Bromo-adenosine 
8-Bromo-guanosine 
T: Sustituted 2'-O-Methyl ribo nucleoside 
2'- O -Methyl-5-iodo-uridine 
2'- O -Methyl-5-methyl-cytidine 
2'- O -Methyl-5-propynyl-cytidine 
2'- O -Methyl-5-propynyl-uridine 
2'- O -Methyl- N 6-dimethyl-adenosine 
β -L-2'- O -Methyl-2-amino-adenosine 
β -L-2'- O -methyl-uridine 
U: Sustituted 3'-O-Methyl ribo nucleoside 
3'- O -Methyl-5-methyl-cytidine 
V: Iso ribo nucleoside 
Iso-2'-deoxyguanosine

Base ( N -protected) mononucleosides: I-Base (N -protected) deoxy mononucleosides

A: Standard and Labile deoxy nucleosides 
2'-Deoxyadenosine ( N -Bz) 
2'-Deoxyadenosine ( N -DMF) 
2'-Deoxyadenosine ( N -PAC) 
2'-Deoxycytidine ( N -Ac) 
2'-Deoxycytidine ( N -Bz) 
2'-Deoxycytidine ( N -iBu) 
2'-Deoxycytidine ( N -PAC) 
2'-Deoxyguanosine ( N -DMF) 
2'-Deoxyguanosine ( N -iBu) 
2'-Deoxyguanosine ( N -PAC) 
B: 5’-Levulinyl deoxy Nucleoside 
5’-Levulinyl-2'-deoxyadenosine ( N -Bz) 
5’-Levulinyl-2'-deoxycytidine ( N -Bz) 
5’-Levulinyl-2'-deoxyguanosine ( N -iBu) 
5’-Levulinyl-2'-deoxythymidine 
C: 3'-Levulinyl deoxy Nucleosides 
3’-Levulinyl-2'-deoxyadenosine ( N -Bz) 
3’-Levulinyl-2'-deoxycytidine ( N -Bz) 
3’-Levulinyl-2'-deoxyguanosine ( N -iBu) 
3’-Levulinyl-2'-deoxythymidine 
D: 3'- O -Acetyl deoxy Nucleosides 
3’- O -Acetyl-2'-deoxyadenosine ( N -Bz) 
3’- O -Acetyl-2'-deoxycytidine ( N -Bz) 
3’- O -Acetyl-2'-deoxyguanosine ( N -iBu) 
3’- O -Acetyl-2'-deoxyuridine 
3’- O -Acetyl-2'-thymidine

Base ( N -protected) mononucleosides: II-Base ( N -protected) ribo mononucleosides

A: Standard and Labile ribo nucleosides 
Aadenosine ( N -isopentyl) 
Adenosine ( N -Bz) 
Adenosine ( N -PAC) 
Cytidine ( N -Ac) 
Cytidine ( N -Bz) 
Cytidine ( N -iBu) 
Cytidine ( N -PAC) 
Guanosine ( N -iBu) 
Guanosine ( N -PAC) 
Guanosine ( N -phenyl acetyl) 
B: 5',3'-Tetraisopropyl disiloxane ribo Nucleoside 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Adenosine ( N -Bz) 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Adenosine ( N -iBu) 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Cytidine  ( N -Ac) 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Cytidine ( N -iBu) 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)e-Adenosine ( N -PAC) 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Guanosine  ( N -Ac) 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Guanosine  ( N -iBu) 
5',3'- O -(1,1,3,3-Tetraisopropyl-1,3-disiloxanediyl)-Guanosine ( N -DMF) 
C: 2', 3'-isopropylene ribo nucleosides 
2',3'-Isopropylidene-guanosine  ( N -iBu) 
2',3'-Isopropylidene-Adenosine ( N -Bz) 
2',3'-Isopropylidene-uridine 
D: 2',3'-Diacetyl ribo Nucleosides 
2',3'-Diacetyl-adenosine ( N -Bz) 
2',3'-Diacetyl-cytidine ( N -Ac) 
2',3'-Diacetyl-cytidine ( N -Bz) 
2',3'-Diacetyl-guanosine ( N -iBu) 
2',3'-Diacetyl-thymidine 
2',3'-Diacetyl-uridine 
E: Modified ribo Nucleosides ( N -alkylated, 2,2’-Anhydro, 3’-( O -Allyl), 5-Methyl & Iso) 
2,2’-Anhydro-5-methyl-cytidine ( N -Bz) 
3’-( O -Allyl)-cytidine ( N -Bz) 
5-Methyl-cytidine ( N -Bz) 
Adenosine ( N -Ethyl) 
Iso-guanosine ( N -DBF)

DMT Protected mononucleoside: I-DMT Protected deoxy Mononucleoside

A: Deoxy mononucleosides with Standard and Labile protection 
5'- O -DMTr-2'-deoxyadenosine ( N 6 - t -Butyl-Phenoxy-Ac) 
5'- O -DMTr-2'-deoxyadenosine ( N -Ac) 
5'- O -DMTr-2'-deoxyadenosine ( N -Bz) 
5'- O -DMTr-2'-deoxyadenosine ( N -Fmoc) 
5'- O -DMTr-2'-deoxyadenosine ( N -iBu) 
5'- O -DMTr-2'-deoxyadenosine ( N -PAC) 
5'- O -DMTr-2'-deoxycytidine ( N 4-t-Butyl-Phenoxy-Ac) 
5'- O -DMTr-2'-deoxycytidine ( N -Ac) 
5'- O -DMTr-2'-deoxycytidine ( N -Bz) 
5'- O -DMTr-2'-deoxycytidine ( N -Fmoc) 
5'- O -DMTr-2'-deoxycytidine ( N -iBu) 
5'- O -DMTr-2'-deoxycytidine ( N -PAC) 
5'- O -DMTr-2'-deoxyguanosine ( N -Fmoc) 
5'- O -DMTr-2'-deoxyguanosine ( N -iBu) 
5'- O -DMTr-2'-deoxyguanosine ( N -isopropyl-PAC) 
5'- O -DMTr-2'-deoxyguanosine ( N -PAC) 
5'- O -DMTr-2'-deoxyguanosine ( N -tBPAC) 
5'- O -DMTr-2'-deoxyinosine 
5'- O -DMTr-2'-deoxyuridine 
5'- O -DMTr-Thymidine 
B: 7-Deaza deoxy nucleosides 
7-Deaza-5'- O -DMTr-deoxyadenosine ( N -Bz) 
7-Deaza-5'- O -DMTr-deoxyguanosine ( N -iBu) 
7-Deaza-5'- O -DMTr-deoxyinosine 
C: Halogenated deoxy nucleosides 
5-Bromo-5'- O -DMTr-deoxyuridine 
5-Iodo-5'- O -DMTr-deoxycytidine ( N -DBF) 
5-Iodo-5'- O -DMTr-deoxyuridine 
8-Bromo-5'- O -DMTr-deoxyadenosine ( N -Bz) 
8-Bromo-5'- O -DMTr-deoxyadenosine ( N -DBF) 
8-Bromo-5'- O -DMTr-deoxyguanosine ( N -iBu) 
D: 5-Alkylated deoxy nucleosides 
5-Methyl-5'- O -DMTr-deoxycytidine ( N -Bz) 
5-Propynyl-5'- O -DMTr-deoxycytidine ( N -Bz) 
5-Propynyl-5'- O -DMTr-deoxyuridine 
E:  N -Alkylated deoxy Modified Nucleosides 
N 3 -Methyl-5'- O -DMTr-thymidine 
N 6 -Methyl-5'- O -DMTr-deoxyadenosine 
N -Cyanoethyl-5'- O -DMTr-deoxycytidine 
N 3 -Cyanoethyl-5'- O -DMTr-thymidine 
F: Iso deoxy modified nucleoside 
Iso-5'- O -DMTr-deoxyguanosine ( N- DBF) 
G: 3'-substituted deoxy modified nucleosides 
3'-Azido-5'- O -DMTr-7-deaza-7-propargylamino (TFA)-2'-deoxyguanosine ( N -PAC)

DMT Protected mononucleoside: II-DMT Protected ribo Mononucleosides

A: ribo mononucleosides with Standard and Labile protection 
5'- O -DMTr-Adenosine ( N -Bz) 
5'- O -DMTr-Adenosine ( N -Fmoc) 
5'- O -DMTr-Adenosine ( N -PAC) 
5'- O -DMTr-Cytidine ( N -Ac) 
5'- O -DMTr-Cytidine ( N -Bz) 
5'- O -DMTr-Cytidine ( N -Fmoc) 
5'- O -DMTr-Cytidine ( N -iBu) 
5'- O -DMTr-Cytidine ( N -PAC) 
5'- O -DMTr-Guanosine ( N -Ac) 
5'- O -DMTr-Guanosine ( N -Fmoc) 
5'- O -DMTr-Guanosine ( N -iBu) 
5'- O -DMTr-Guanosine ( N -isopropyl-PAC) 
5'- O -DMTr-Guanosine ( N -PAC) 
5'- O -DMTr-Inosine 
5'- O -DMTr-Thymidine 
5'- O -DMTr-Uridine 
B:  2'-O-Methyl ribo nucleosides 
2'- O -Methyl-5'- O -DMTr-adenosine ( N -Bz) 
2'- O -Methyl-5'- O -DMTr-adenosine ( N -PAC) 
2'- O -Methyl-5'- O -DMTr-cytidine ( N -Ac) 
2'- O -Methyl-5'- O -DMTr-cytidine ( N -Bz) 
2'- O -Methyl-5'- O -DMTr-cytidine ( N -PAC) 
2'- O -Methyl-5'- O -DMTr-guanosine ( N -iBu) 
2'- O -Methyl-5'- O -DMTr-guanosine ( N -PAC) 
2'- O -Methyl-5'- O -DMTr-uridine 
C: 2'-O-TBDMS  ribo modified nucleosides 
2'- O -TBDMS-5'- O -DMTr-adenosine ( N -diBz) 
2'- O -TBDMS-5'- O -DMTr-adenosine ( N -Bz) 
2'- O -TBDMS-5'- O -DMTr-adenosine ( N -PAC) 
2'- O -TBDMS-5'- O -DMTr-cytidine ( N -Ac) 
2'- O -TBDMS-5'- O -DMTr-cytidine ( N -Bz) 
2'- O -TBDMS-5'- O -DMTr-cytidine ( N -PAC) 
2'- O -TBDMS-5'- O -DMTr-guanosine ( N -DMF) 
2'- O -TBDMS-5'- O -DMTr-guanosine ( N -iBu) 
2'- O -TBDMS-5'- O -DMTr-guanosine ( N -iPrPAC) 
2'- O -TBDMS-5'- O -DMTr-guanosine ( N -PAC) 
2'- O -TBDMS-5'- O -DMTr-inosine 
2'- O -TBDMS-5'- O -DMTr-uridine 
D: 3'-O-TBDMS  ribo modified nucleosides 
3'- O -TBDMS-5'- O -DMTr-Adenosine ( N -Bz) 
3'- O -TBDMS-5'- O -DMTr-Cytidine ( N -Bz) 
3'- O -TBDMS-5'- O -DMTr-Guanosine ( N -iBu) 
3'- O -TBDMS-5'- O -DMTr-Uridine 
3'- O -TBDMS-5'- O -DMTr-Cytidine ( N -Ac) 
E: 2’-O-Methyl-5-Alkylated ribo nucleosides 
2'- O -Methyl-5-methyl-5'- O -DMTr-cytidine ( N -Bz) 
2'- O -Methyl-5-methyl-5'- O -DMTr-uridine 
2'- O -Methyl-5-propynyl-5'- O -DMTr-cytidine ( N -Bz) 
2'- O -Methyl-5-propynyl-5'- O -DMTr-uridine 
F: 5-Alkylated ribo modified nucleosides 
5-Methyl-5'- O -DMTr-cytidine ( N -Bz) 
5-Propynyl-5'- O -DMTr-cytidine ( N -Bz) 
5-Propynyl-5'- O -DMTr-uridine 
G: Modified purine ribo nucleosides 
5'- O -DMTr-Purine-riboside ( N 6 -DMF) ( N 2 -iBu) 
H: Halogenated ribo nucleosides 
8-Bromo-5'- O -DMTr-adenosine ( N -DBF)