Modified Nucleotides

Dna sofware supports user to simulate and design assays with wide variety of modified nucleotides. Below are the supported modified nucleotides.

Supported 5 Letter codes in DNA

DNA_I = deoxyInosine
DNA_U = deoxyUridine
DisoC = isoC with deoxy sugar
DisoG = isoG with deoxy sugar
D_DAP = DiAminoPurine in DNA

D_gcC = G-clamp C in DNA
D_2fC = 2′ fluoroC in DNA
D_2fU = 2′ fluoroU in DNA
D_5mC = 5-methyl-C in DNA
D_5pC = 5-propynyl-C in DNA
D_5pU = 5-propynyl-U in DNA
D_2tT = 2-thio Thymine in DNA
D_2ap = 2-amino purine in DNA
DNA_Z = 7-deazaG in DNA
OM2_A = 2′-O-methyl adenosine
OM2_C = 2′-O-methyl cytidine
OM2_G = 2′-O-methyl guanosine
OM2_U = 2′-O-methyl uridine

LNA_A = LNA adenosine
LNA_C = LNA cytidine
LNA_G = LNA guanosine
LNA_T = LNA Thymidine
LNA_U = LNA uridine
RNA_A = RNA adenosine chimeric in DNA
RNA_C = RNA cytidine chimeric in DNA
RNA_G = RNA guanosine chimeric in DNA
RNA_U =RNA uridine chimeric in DNA

Future Releases in DNA

D_2fA = 2′ fluoroA in DNA
D_2fG = 2′ fluoroG in DNA
D_2fT = 2′ fluoroT in DNA

Within RNA the following 5-letter codes are supported:

RNA_T = RNA backbone with Thymidine base
OM2_A = 2′-O-methyl adenosine
OM2_C = 2′-O-methyl cytidine
OM2_G = 2′-O-methyl guanosine
OM2_U = 2′-O-methyl uridine
DNA_A = DNA adenosine chimeric in RNA
DNA_C = DNA cytidine chimeric in RNA
DNA_G = DNA guanosine chimeric in RNA
DNA_T =DNA thymidine chimeric in RNA
LNA_A = LNA adenosine
LNA_C = LNA cytidine

LNA_G = LNA guanosine
LNA_T = LNA Thymidine
LNA_U = LNA uridine
D_2fC = 2′ fluoroC with DNA backbone
D_2fU = 2′ fluoroU with DNA backbone
D_5pC = 5-propynyl-C with DNA backbone
D_5pU = 5-propynyl-U with DNA backbone
RisoC = isoC in RNA
RisoG = isoG in RNA
R_DAP = DiAminoPurine in RNA
R_5mC = 5-methyl-C in RNA
RNA_Z = 7-deazaG in RNA

Future Releases in RNA

PSD_A = Phosphorothioate A with DNA sugar chimeric in RNA
PSD_C = Phosphorothioate C with DNA sugar chimeric in RNA
PSD_G = Phosphorothioate G with DNA sugar chimeric in RNA
PSD_T = Phosphorothioate T with DNA sugar chimeric in RNA

Within PNA the following 5-letter codes are supported:

PNA_Z = 7-deazaG in PNA
P_DAP = diaminopurine in PNA
PNA Fluorophores and quenchers: 5’-Texas Red, 5’-Cy3, 3’-BHQ, 3’-TAMRA

Within MOR the following 5-letter codes are supported:

No modifieds allowed
Fluorophores allowed: 3’-Lissamine, 3’-FAM, 3’-Dabcyl, 3’-Biotin.

For DNA and RNA here are the 3′-quenchers and 5′-Fluorophores that we support.
  • Click this link to check out the supported Fluorohores and Quenchers
  • There is also support for terminal phosphate, biotin, certain PEG linkers
  • We also have some support for internal fluorophores (inquire if interested).