How a sequence is written
Oligonucleotide notation
The AUM notation writes an oligonucleotide as one line of text. The bases run 5' to 3', and a tag before a base gives its sugar. An asterisk marks a phosphorothioate linkage, and a code in braces marks a modification.
The sequence builder on the order page writes it, and the cart, the quotation and the account print the same line.
The rules
Bases, sugars, linkages and modifications
- Direction
- A sequence is written 5' to 3'.
- Bases
- A capital A, C, G or T with no tag before it is a DNA base. U is uracil and follows a sugar tag, as in rU or mU. N is the degenerate base, written as a plain letter with no tag.
- Sugars
- A lower-case tag before a base gives its sugar. The tags are r for RNA, m for 2'-O-methyl (2'-OMe), moe for 2'-O-methoxyethyl (2'-MOE), l for locked nucleic acid and f for 2'-fluoro. DNA takes no tag.
- Linkages
- An asterisk between two bases is a phosphorothioate linkage. Two bases with nothing between them are joined by a phosphodiester linkage.
- Modifications
- A modification is its code in braces, written where it sits. At the start of the sequence it is on the 5' end, and at the end on the 3' end. Between two bases it is internal. A modification that replaces a base is written in place of that base.
Sugars
Sugar tags
One tag per sugar, written directly before the base it belongs to.
| Sugar | Tag | Written as |
|---|---|---|
| DNA | no tag | A |
| RNA | r | rA |
| 2'-O-methyl (2'-OMe) | m | mA |
| 2'-O-methoxyethyl (2'-MOE) | moe | moeA |
| locked nucleic acid | l | lA |
| 2'-fluoro | f | fA |
Modifications
Modification codes
Every modification the site offers, with the code the notation writes it by and where it may sit.
Ends and phosphates
| Code | Modification | Position |
|---|---|---|
| {Phos} | Phosphate | 5' end, 3' end |
| {Diphos} | 5'-diphosphate | 5' end |
| {Triphos} | 5'-triphosphate | 5' end |
| {App} | 5'-adenylation (rApp) | 5' end |
| {Puromycin} | Puromycin | 3' end |
| {Cyclic-Phos} | 2',3'-cyclic phosphate | 3' end |
| {2'-Phos} | 2'-phosphate | 3' end |
| {VP} | 5'-vinylphosphonate (PS) | 5' end |
Linkers and click handles
| Code | Modification | Position |
|---|---|---|
| {Amino-C6} | Amino linker C6 | 5' end, 3' end |
| {Thiol-C6} | Thiol linker C6 (S-S) | 5' end, 3' end |
| {Azide} | Azide | 5' end, 3' end |
| {Alkyne} | 5'-hexynyl (alkyne) | 5' end |
| {DBCO} | DBCO-TEG | 5' end |
Spacers
| Code | Modification | Position |
|---|---|---|
| {Spacer-9} | Spacer 9 | 5' end, 3' end, internal |
| {Spacer-18} | Spacer 18 | 5' end, 3' end, internal |
| {Spacer-C6} | C6 spacer | 5' end, 3' end, internal |
| {Spacer-C3} | C3 spacer | 5' end, 3' end, internal |
Dyes
| Code | Modification | Position |
|---|---|---|
| {FAM} | 6-FAM | 5' end, 3' end |
| {Cyanine-3} | Cyanine 3 | 5' end, 3' end, internal |
| {Cyanine-5} | Cyanine 5 | 5' end, 3' end, internal |
| {Cyanine-7} | Cyanine 7 | 5' end, 3' end, internal |
| {TAMRA} | TAMRA | 5' end, 3' end |
| {ROX} | ROX | 5' end, 3' end |
| {HEX} | HEX | 5' end, 3' end |
| {JOE} | JOE | 5' end, 3' end |
Quenchers
| Code | Modification | Position |
|---|---|---|
| {Dabcyl} | Dabcyl | 5' end, 3' end |
Conjugates
| Code | Modification | Position |
|---|---|---|
| {Biotin} | Biotin | 5' end, 3' end, internal |
| {Cholesterol-TEG} | Cholesterol-TEG | 5' end, 3' end |
| {Psoralen-C6} | Psoralen C6 | 5' end |
| {Digoxigenin} | Digoxigenin | 5' end, 3' end |
| {GalNAc} | GalNAc (extendable) | 5' end |
| {Palmitate} | Palmitate | 5' end, 3' end |
| {Tocopherol-TEG} | Tocopherol-TEG | 5' end, 3' end |
Modified bases
| Code | Modification | Position |
|---|---|---|
| {Inverted-dT} | Inverted dT | 3' end |
| {Carboxy-dC} | Carboxy-dC | internal, in place of a C |
| {AZT} | AZT | 3' end |
| {Biotin-dT} | Biotin-dT | internal, in place of a T |
| {Amino-C6-dT} | Amino-C6-dT | internal, in place of a T |
| {Amino-dC} | Amino-dC | internal, in place of a C |
| {Dabcyl-dT} | Dabcyl-dT | internal, in place of a T |
| {dU} | Deoxyuridine (dU) | internal, in place of a T |
| {dI} | Deoxyinosine (dI) | internal, in place of any base |
| N | Degenerate base (N) | internal, in place of any base |
| {5-Me-dC} | 5-methyl-dC | internal, in place of a C |
| {ddC} | 3'-dideoxy-C | 3' end |
Examples
Worked examples
{Phos}mG*mC*A*T*T*C*A*G*mU*mC{Biotin}A 5' phosphate, 2 bases of 2'-OMe, 6 of DNA and 2 of 2'-OMe on a phosphorothioate backbone, and biotin on the 3' end.
moeG*moeC*moeA*moeT*moeT*C*A*G*T*C*A*G*T*C*A*moeG*moeC*moeA*moeT*moeT
A 5-10-5 gapmer: 5 bases of 2'-MOE, 10 of DNA and 5 of 2'-MOE, every linkage phosphorothioate.
{FAM}ACGTTAGCCATG{Dabcyl}A probe: FAM on the 5' end, 12 DNA bases on phosphodiester linkages, Dabcyl on the 3' end.
GT{5-Me-dC}GATCCA DNA oligonucleotide with 5-methyl-dC in place of its third base.
The order page reads this notation and the common forms of other suppliers. Those forms are slash codes, bracket codes, and the m, r, e, l, f and + prefixes before a base. An asterisk or an s marks a phosphorothioate linkage in any of them. It writes what it read in this notation, and a code it does not know is written on the quotation as typed.
Your sequence, on the order page
The order page takes one sequence as a quotation line, and bulk synthesis takes a list of them.
For research use only. Not for use in diagnostic or therapeutic procedures.