Modified Nucleotide Library

Modified nucleotides are accessed by 2 mechanisms:

1. Declaration of the strand type using the keyword

“SEQUENCE_TYPE=value” (e.g. SEQUENCE_TYPE=MOR). There are six strand types that we support (your current version supports all of these):

  • DNA = deoxyribonucleic acid
  • RNA = ribonucleic acid
  • PNA = peptide nucleic acids
  • MOR = morpholino backbone
  • PSD = phosphorothioate with deoxy ribose sugar OM2 = 2′-O-methyl-RNA

2. Declaration of a chimeric modified nucleotide within a sequence of a particular strand type. The modified nucleotides are specified by a 5-letter code enclosed within a curly bracket, as follows:

SEQUENCE_TYPE=DNA
SEQUENCE = CAGCAGCTC{DNA_I}AGA{OM2_G}CTCGC //a DNA sequence with two chimeric modifications

Here is the complete list of supported 5 letter codes for each of the strand types.

A. Within DNA the following 5-letter codes are supported:

  • 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

B. 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

RNA in the future will support:

  • 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

C. 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

D. Within MOR the following 5-letter codes are supported:

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

E. For DNA and RNA here are the 3′-quenchers and 5′-Fluorophores that we support. There is also support for terminal phosphate, biotin, certain PEG linkers. We also have some support for internal fluorophores (inquire if interested). Here is the complete list of Fluorophores and quenchers:

3′-Quenchers:

  • BHQ-1 (Black Hole Quencher 1)
  • BHQ-2 (Black Hole Quencher 2)
  • Dabcyl
  • Iowa Black FQ 420-620 max 531
  • Iowa Black RQ 500-700 max 656
  • QSY 7 amine
  • QSY 9 hydrazide
  • QSY 35 methylamine

5′ Fluorophores:

  • Alexa Fluor 350 cadaverine
  • Alexa Fluor 430 cadaverine
  • Alexa Fluor 488 cadaverine
  • Alexa Fluor 532 cadaverine
  • Alexa Fluor 546 cadaverine
  • Alexa Fluor 568 cadaverine
  • Alexa Fluor 594 cadaverine
  • Alexa Fluor 633 cadaverine
  • Alexa Fluor 660 cadaverine
  • Alexa Fluor 680 cadaverine
  • Bodipy 630/650-X NHS Ester
  • Bodipy 650/665-X NHS Ester
  • 7-diethylaminocoumarin-3-carboxylic acid
  • Cy-2 (Cyanine 2)
  • Cy-3 (Cyanine 3)
  • Cy-3.5 (Cyanine 3.5)
  • Cy-5 (Cyanine 5)
  • Cy-5.5 (Cyanine 5.5)
  • Cycler 640
  • DY547
  • DY647
  • DY677
  • FAM (Fluorescein Amidite)
  • HEX (Hexachlorofluorescein)
  • VIC
  • Dimethoxyfluorescein
  • Lissamine
  • MGB (Minor Groove Binder)
  • Oregon Green 488-X NHS Ester
  • Oregon Green 514 NHS Ester Pyrene
  • Rhodamine Green NHS Ester
  • Rhodamine Red NHS Ester
  • 6-carboxy-X-rhodamine
  • Carboxytetramethylrhodamine
  • TET (Tetrachlorofluorescein)
  • Texas 615
  • Texas Red cadaverine
  • Texas Red-OO
  • TYE 563
  • TYE 665