Internal/nucleosidic modifications

Internal/nucleosidic modifications** 5' 3' Internal Cat. no. Comments
Adenosines
2-Amino-2'-dA     5-0230-01X For increase of melting temperature
2Amino2dA

2-Amino-2'-deoxyadenosine

  • Increases melting temperature by 3°C per 2-Amino-2'-dA/dT base pair 
3'-dA(Cordycepin)     5-0230-21X For blocking 3’-end
3dA

3'-Deoxyadenosine (Cordycepin)

  • For blocking the 3'-end of oligonucleotides from extension or ligation 
7-Deaza-2'-dA     5-0230-31X For reducing secondary structure formation
7Deaza2dA

7-Deaza-2'-deoxyadenosine

  • Incorporation of 7-Deaza-2'-dA can reduce secondary structures
8-Bromo-2'-dA     5-0230-41X For crystallographic studies
8bromo2dA

8-Bromo-2'-deoxyadenosine

  • Halogenated nucleosides are useful for crystallographic studies
  • Useful for probing the structure of Protein-RNA, Protein-DNA and DNA-RNA complexes in crosslinking experiments
N6-Methyl-2'-dA     5-0230-51X To study/use methylation effects
N6Me2dA

N6-Methyl-2'-deoxyadenosine

  • For studies on methylation effects 
  • For blocking of restriction enzymes
Cytidines
2', 3'-ddC     5-0231-01X For blocking the extension of oligonucleotides
23ddC

2',3'-Dideoxycytidine

  • Useful for blocking the extension of oligonucleotides e.g. during PCR 
  • No substrate for RNA- and DNA-ligases
5-Me-2'-dC     5-0231-11X For increase of melting temperature
5Me2dC

5-Methyl-2'-deoxycytidine

  • Increases melting temperature by 1.3°C per 5-Methyl-2'-dC/dG base pair 
5-Bromo-2'-dC     5-0231-21X For crystallographic studies
5Br2dC

5-Bromo-2'-deoxycytidine

  • Halogenated nucleosides are useful for crystallography 
  • Useful for probing the structure of Protein-RNA, Protein-DNA and DNA-RNA complexes in crosslinking experiments
5-C6-Amino-2’-dC     5-0231-32X For internal amino group incorporation
5c6Amino2dC

5-C6-Amino-2'deoxycytidine 

  • Useful for the attachment of internal labels
5-Carboxy-dC     5-0233-12X For DNA damage and repair research
5-Carboxy-dC-CEP

5-Carboxy-dC is used in DNA damage, DNA repair and epigenetics researches.

5-Formyl-dC     5-0233-60X For probing the process of DNA demethylation
5-Formyl-dC-CEP

5-Formyl-dC is highly mutagenic and also used in epigenetic researches as a tool for probing the DNA demethylation process.

5-Hydroxymethyl-dC     5-0517-11X For DNA methylation
5-Hydroxymethyl-dC-CEP

5-Hydroxymethyl-dC is used in DNA methylation studies, DNA damage and epigenetics researches.

5-Hydroxymethyl-dC II     5-0517-12X For DNA methylation
5-Hydroxymethyl-dC II CEP

5-Hydroxymethyl-dC II is used in DNA methylation studies, DNA damage and epigenetics researches.

N-4-TriGl-Amino-2’dC     5-0231-33X For internal amino group incorporation
N4TriGlAmino2dC

N4-TriGl-Amino 2'deoxycytidine (N4-Amino dC)

  • Useful for the attachment of internal labels
5-Iodo-2'-dC     5-0231-31X For crystallographic studies
5Iodo2dC

5-Iodo-2'-deoxycytidine

  • Halogenated nucleosides are useful for crystallography
  • Useful for probing the structure of Protein-RNA, Protein-DNA and RNA-RNA complexes in crosslinking experiments
C8-Alkyne-dC     5-0233-24X For alkyne modification of oligos
C8-Alkyne-dC-CEP

C8-Alkyne-dC is used for alkyne modification of oligos that can then be labeled or modified by click chemistry.

C8-TIPS-dC     5-0233-25X For conjugation using click chemistry
C8-TIPS-dC-CEP

C8-TIPS-dC is used for alkyne modification of oligos that can then be labeled or modified by click chemistry.

C8-TMS-dC     5-0233-26X For coupling
C8-TMS-dC-CEP

C8-TMS-dC is used for alkyne modification of oligos that can then be labeled or modified by click chemistry.

N4-Ethyl-dC     5-0231-41X To study/use methylation effects
N4EthyldC

N4-Ethyl-deoxycytidine

  • Used in immune stimulation experiments
3'-dC     5-0231-51X For blocking 3’-end
3-dC

3'-Deoxycytidine

  • Inhibition of RNA polymerase
  • Used in RNA research
5-OH-dC     5-0233-70X For DNA damage and repair research
5-OH-dC-CEP

5-hydroxy deoxycytosine (5-OH-dC) is used in oxidative DNA damage and DNA repair mechanisms especially. It's especially being used in studies for tumorigenesis and the process of aging. 

Guanosines
7-Deaza-2'-dG     5-0232-01X For reducing secondary structure formation
7Deaza2dG

7-Deaza-2'-deoxyguanosine

  • Incorporation of 7-Deaza-2'-dG can reduce secondary structures 
  • Incorporation of 7-Deaza-2'-dG prevents formation of G-tetrades 
8-Bromo-2'-dG     5-0232-11X For crystallographic studies
8Bromo2dG

8-Bromo-2'-deoxyguanosine

  • Halogenated nucleosides are useful for crystallography  
  • Useful for probing the structure of Protein-RNA, Protein-DNA and DNA-RNA complexes in crosslinking experiments
Thymidines
4-Thio-dT     5-0233-01X For cross-linking
4ThiodT

4-Thio-2'-deoxythymidine

  • Useful in cross-linking and affinity-labeling experiments
5-C3-Carboxy-dT     5-0233-11X For coupling
5C3CarbodxydT

5-C3-Carboxy-2'-deoxythymidine

  • Useful for introduction of molecules with a primary amine such as antibodies and enzymes by standard coupling procedures 
5-C6-Amino-dT     5-0233-21X For internal amino-group incorporation
5C6AminodT

5-C6-Amino-2'-deoxythymidine 

  • Incorporation of internal reporter groups 
  • Does not interfere with nucleic acid hybridization 
  • Unique ability to provide functional amino groups at internal sites 
5-C2-Amino-dT     5-0233-22X For internal amino-group incorporation
5c2aminodt

5-C2-Amino-2'-deoxythymidine 

  • Incorporation of large molecules
  • Does not interfere with hybridization characteristics
  • Structure on the right: 5-C2-Amino-2'-deoxythymidine*
Inverse-dT     5-0233-31X For blocking oligos against extension and ligation
InversedT

Inverse-2'-deoxythymidine

  • For blocking oligonucleotides from extension or ligation 
  • Stabilization against 3'-exonucleases  
N3-Cyanoethyl-dT     5-0233-50X For synthesis of oligodeoxynucleotides (ODNs)
N3-Cyanoethyl-dT

N3-Cyanoethyl-dT is used for synthesis of oligodeoxynucleotides (ODNs).

Special RNA modifications

2'-NH2-RNA     5-0511-01X For stabilization against nucleases
2NH2RNA

2'-Amino-modified RNA oligonucleotides 

  • Stabilization against nucleases 
  • 2'-Amino-rU and 2'-Amino-rC available 
  • Number of couplings are limited due to poor coupling efficiency 
2'-F-RNA     5-0512-01X For stabilization against nucleases; increase of melting temperature
2FRNA

2'-Fluoro-modified RNA oligonucleotides 

  • Stabilization against nucleases 
  • Increase of melting temperature by 2°C per residue
  • 2'-F-RNA/RNA duplexes are no substrates for RNase H
  • Only 2'-F-rU and 2'-F-rC available 
2'-O-Methyl-RNA     5-0513-01X For stabilization against nucleases; increase of melting temperature
2omeRNA

2'-O-Methyl-modified RNA oligonucleotides

  • Provides stabilization against nucleases 
  • Increases melting temperature by 1.5°C per residue
  • 2'-O-Methyl-RNA/RNA hybrids are not recognized by RNase H  
  • Important for antisense applications 
Inosine ribo     5-0514-01X For ribozyme technology
Inosineribo

Inosine-modified RNA oligonucleotides

  • Special application in ribozyme technology 
  • Changes ribozyme cleavage specifity from NUH to NCH
Other modifications
2-Aminopurin     5-0230-60X For structural analysis
2Aminopurin

2-Aminopurine

  • Used in mutagenesis, transcriptional regulation, nucleic acid structure and dynamics experiments
Abasic-Alkyne     5-0230-63X For alkyne modification of oligos
Abasic-Alkyne-CEP

Abasic-Alkyne is used for alkyne modification of oligos that can then be labeled or modified by click chemistry.

Spacer 3 5-0210-92X For introducing a linker arm
Spacer C3

Spacers are used to insert a spacer arm in an oligonucleotide. The enlarged space via the spacer can avoid the steric hindrance of the dyes or modifications that are introduced to the oligonucleotide ends or can block the oligo ends from enzymatic reactions.

Spacer 6 5-0210-95X For introducing a linker arm
Spacer C6

Spacers are used to insert a spacer arm in an oligonucleotide. The enlarged space via the spacer can avoid the steric hindrance of the dyes or modifications that are introduced to the oligonucleotide ends or can block the oligo ends from enzymatic reactions.

Spacer 9 5-0210-96X For introducing a linker arm
Spacer9

Spacers are used to insert a spacer arm in an oligonucleotide. The enlarged space via the spacer can avoid the steric hindrance of the dyes or modifications that are introduced to the oligonucleotide ends or can block the oligo ends from enzymatic reactions.

Spacer 12 5-0210-97X For introducing a linker arm
Spacer12 CEP

Spacers are used to insert a spacer arm in an oligonucleotide. The enlarged space via the spacer can avoid the steric hindrance of the dyes or modifications that are introduced to the oligonucleotide ends or can block the oligo ends from enzymatic reactions.

Spacer 18 5-0210-98X For introducing a linker arm
Spacer18 CEP

Spacers are used to insert a spacer arm in an oligonucleotide. The enlarged space via the spacer can avoid the steric hindrance of the dyes or modifications that are introduced to the oligonucleotide ends or can block the oligo ends from enzymatic reactions.

Stable abasic site     5-0230-61X One base spacer
Stableabasicsite

Stable abasic site

  • One base spacer for oligonucleotides
Stable ribo abasic site (rSpacer)     5-0230-62X One base spacer
RSpacer
2'-dI (2'-Deoxyinosine)     5-0234-01X For increasing base pairing
2dI

2'-Deoxyinosine

2´-Deoxyinosine (2´-dI) in an oligonucleotide is used for wobble positions, since it can form base pairs with all bases. As a specialty, we are able to introduce as many inosines as you require into one oligonucleotide! Several experiments have suggested that deoxyinosine might be an "inert" base; its presence in an oligonucleotide sequence seems neither to disturb DNA duplex formation nor to destabilize the duplex. Deoxyinosine containing primers have been used successfully to amplify cDNA or genomic fragments for the generation of DNA probes from a peptide sequence.

  • 2´-dI can form base pairs with A, G, C and T*  
  • useful when parts of your target sequence are unknown  
  • great for targeting different mutants of a gene  
  • 50% discount if more than 5 inosine modifications are requested in one order! 

* the order of stabilities of base pairings is I-C >> I-A > I-T = I-G

2'-dU     5-0235-01X For PCR-product cloning
2dU

2'-Deoxyuridine 

  • Replacement of thymidine with 2'-deoxyuridine results in destabilization of a DNA duplex 
  • Is used in combination with Uracil-DNA glycosylase to avoid cross-contamination of PCR products 
  • Useful for cloning of PCR-products (in combination with Uracil-DNA glycosylase)
5-Fluoro-2'-dU     5-0235-11X For crystallographic studies
5Fluoro2dU

5-Fluoro-2'-deoxyuridine 

  • Halogenated nucleosides are useful for chrystallography 
  • Structure on the right:
5-Bromo-dU coupling     5-0235-13X For crystallographic studies
5brdUCPG

5-Bromo-dU coupling

  • Halogenated nucleosides are useful for chrystallography 
  • Photolabile and used for crosslinking of DNA with proteins for structure researches.
  • Structure: 5-Br-dU-CPG*

* Structure used with permission of Glen Research Corporation

5-Iodo-2-dU-modification     5-0235-21X For crystallographic studies
5IdUCE

5-Iodo-2-dU-modification

  • Halogenated nucleosides are useful for chrystallography 
  • Photolabile and used for crosslinking of DNA with proteins for structure researches.
  • Structure: 5-I-dU-CE Phosphoramidite*

* Structure used with permission of Glen Research Corporation

5-OH-dU     5-0233-80X For DNA damage and repair research
5-OH-dU-CEP

5-hydroxy deoxyuracil (5-OH-dU) is used in oxidative DNA damage and DNA repair mechanisms. It's especially being used in studies for tumorigenesis and the process of aging.

5-Hydroxymethyl-dU     5-0517-13X For DNA base excision repair research
5-Hydroxymethyl-dU-CEP

5-Hydroxymethyl deoxyuridine (5-hm-dU) is used in oxidative DNA damage and DNA repair mechanisms especially in base excision repair research. It's also used as a deamination intermediate in studies for demethylation in epigenetic regulation.

C8-Alkyne-dU     5-0233-23X For alkyne modification of oligos
C8-Alkyne-dU-CEP

C8-Alkyne-dU is used for alkyne modification of oligos that can then be labeled or modified by click chemistry.

DBCO-PEG4-NHS     5-0233-27X For copper-free Click reactions
DBCO-PEG4
*: All Oligos are available in 0.05, 0.2 and 1.0 µmol
**: All modified DNA oligonucleotides are HPLC purified at no additional charge.
To order your tailor-made oligo above get in contact with our individual personal assistance provided by nucleic acid chemists and molecular biologists. Your personal contact person from IBA Lifesciences is ready to help you by email or phone (+49 551 50672-222) and will support you in designing your correct oligo sequence and advise you in possible promising labeling and modification combinations. Furthermore our assistance alerts you to create incorrect not functional oligonucleotides before starting the synthesis.