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Home » Oligo Synthesis Applications » Custom DNA Oligo Synthesis » GenScript oligonucleotide codes

Overview

GenScript provides convenient online instant quotation and ordering system to build your desired oligonucleotides for comprehensive applications. It is an integrated system to easily build almost all type of single-stranded oligos, such as DNA and RNA oligos with modification and labeling (dual and multiple labeling), antisense oligonucleotides (phosphorothioate DNA and RNA, 2'-OMe-RNA, 2'-F-RNA), chimeric oligonucleotides, etc.

To best use our online instant quotation and ordering system, please use GenScript defined codes as following:

Backbone & Code

Backbone Special Code Description
DNA Standard DNA Bases (A, C, G, T)
Mixed Bases, expressed in UPPERCASE.
Locked nucleic acid bases (LNA) are entered as '+_'.
Phosphorothioated DNA bases are entered as '_*'
Phosphorothioated LNA bases are entered as '+_*'.
RNA Standard RNA Bases (A, C, G, U)
Mixed Bases, expressed in UPPERCASE.
Chimeric DNA base are entered as 'd_'.
2' O-methyl RNA bases are entered as 'm_'.
Locked nucleic acid bases (LNA) are entered as '+_'.
Phosphorothioated RNA bases are entered as '_*'.
Phosphorothioated 2'-O-methyl RNA bases are entered as 'm_*'.
Phosphorothioated LNA bases are entered as '+_*’.
For 2‘-Fluoro RNA base, please select from the dropbox
Oligo Synthesis

Standard Mixed DNA Bases

Mixed DNA Bases Insert Code
dA+dG+dC+dT (N)
dT+dC+dG (B)
dA+dT+dG (D)
dA+dT+dC (H)
dA+dC+dG (V)
dA+dC (M)
dA+dG (R)
dA+dT (W)
dC+dG (S)
dC+dT (Y)
dT+dG (K)

Custom Mixed DNA Bases

Mixed DNA Bases Insert Code
X1%dA+X2%dC+X3%dG+X4%dT (X1%AX2%CX3%GX4%T)
e.g. 30%dA+30%dC+20%dG+20%dT (30%A30%C20%G20%T)

5' internal and 3' modification/labeling

Classification Modification 5' Mod Code Internal Mod Code 3' Mod Code
Fluorescent labeling
 CY3 /5'CY3/ /iCY3/ /3'CY3/
CY5

 /5'CY5/ /iCY5/ /3'CY5/
FAM /5'FAM/ /iFAM/ /3'FAM/
HEX /5'HEX/ /iHEX/ /3'HEX/
6JOE /5'6JOE/ /i6JOE/ /3'6JOE/
ROX /5'ROX/ /iROX/ /3'ROX/
TAMRA /5'TAMRA/ /iTAMRA/ /3'TAMRA/
TET /5'TET/ /iTET/ /3'TET/
Quenchers
 DABCYL - - /3'DABCYL/
BHQ 1 - - /3'BHQ 1/
BHQ 2 - - /3'BHQ 2/
ECLIPSE - - /3'ECLIPSE/
Non-Fluorescent conjugates
 Biotin /5'Biotin/ /iBiotin/ /3'Biotin/
Biotin TEG /5'BiotinTEG/ /iBiotinTEG/ /3'BiotinTEG/
Dual Biotin /5'DualBiotin/ /iDualBiotin/ -
Biotin dT /5'BiotindT/ /iBiotindT/ -
PC Biotin /5'PcBiotin/ /iPcBiotin/ -
Digoxin /5'Digoxin/ /iDigoxin/ /3'Digoxin/
Terminal Phosphorylation
 Phosphorylation /5'Phosphate/ N/A /3'Phosphate/
Linkers
 Amino Linker C3 /5'AminoC3/ /iAminoC3/ /3'AminoC3/
Amino Linker C6 /5'AminoC6/ /iAminoC6/ /3'AminoC6/
Amino Linker C7 /5'AminoC7/ /iAminoC7/ /3'AminoC7/
Amino Linker C12 /5'AminoC12/ /iAminoC12/ /3'AminoC12/
Amino Linker C6 dT /5' AminoC6dT/ /iAminoC6dT/ /3' AminoC6dT/
Disulfide Linker C3 /5'C3 S-S/ /iC3 S-S/ /3'C3 S-S/
Disulfide Linker C6 /5'C6 S-S/ /iC6 S-S/ /3'C6 S-S/
Spacers
 Spacer C3 /5'SpacerC3/ /iSpacerC3/ /3'SpacerC3/
Spacer C6 /5'SpacerC6/ /iSpacerC6/ /3'SpacerC6/
Spacer 9 /5'Spacer9/ /iSpacer9/ /3'Spacer9/
Spacer 18 /5'Spacer18/ /iSpacer18/ /3'Spacer18/
dSpacer /5'dSpacer/ /idSpacer/ /3'dSpacer/
Modified bases
 DeoxyInosine /5'deoxyI/ /ideoxyI/ /3'deoxyI/
DeoxyUridine /5'deoxyU/ /ideoxyU/ /3'deoxyU/
2'-Fluoro A /5'fA/ /ifA/ /3'fA/
2'-Fluoro C /5'fC/ /ifC/ /3'fC/
2'-Fluoro G /5'fG/ /ifG/ /3'fG/
2'-Fluoro U /5'fU/ /ifU/ /3'fU/
Electrochemicals
 Ferrocene /5' Ferrocene / /iFerrocene / /3' Ferrocene /

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