Nucleic Acid Modifications
Nucleic Acid Modifications

A wide variety of modifications can be incorporated directly during the synthesis or after synthesis. Certain modifications (notably Digoxigenin and some fluorescent dyes) are not available to be incorporated during synthesis and must be attached to the oligo after synthesis using NHS ester chemistry. NHS esters react with free primary amines and result in stable, covalent attachments. A primary amine is, therefore, added to the oligo during synthesis to permit reaction with the desired NHS ester. The post-synthetic chemical modifications made to an oligonucleotide by using NHS ester modification result in lower yields than direct incorporation of modifications during synthesis. Furthermore, all NHS ester modifications require HPLC purification. PAGE purification is not offered for NHS ester modifications as yields are further decreased and certain modifications can be damaged during PAGE purification.

Don't see the modification you are interested in? Just ask — in most cases we can accommodate your request. And if you require help in choosing the optimal modification, you can consult the experts by contacting us.

Terminus and Internal Modifications
Acridine Aldehyde
Amino modifiers Branching
Carboxy modifiers Chain terminator
Cholesteryl Dendrimer
Glyceryl Phosphorylation
Psoralen Spacer
Thiol 5' Terminal Caps 

Non-radioactive Labelings
Biotin Digoxigenin
2,4-dinitrophenyl (DNP)

Bases with Altered Paring
DNA damage/repair studies DeoxyUridine (dUracil)
Halogenated Bases isoCytosine (iso-dC) and isoGuanosine (iso-dG)
Spiked Oligos Universal Bases
Degenerate Base – Wobble

PCR/Sequencing Utilities
Duplex Effects Chain Terminators

Bases Increasing Duplex Stability
2'-5' Linked Oligonucleotides Methylphosphonate
2'-O-methyl Modified Oligonucleotides Morpholino Oligonucleotides
C-Propyne Analogues Bridged Nucleic Acid (BNA)
C5 - Methyl Analog Phosphorothioate
Chimeric Oligos

Photo Cleavable
PC-Amino PC-Spacer
PC-Biotin PC-Linker


We offer a personalized solutions to assist client cross link various molecules and compound and solid support attachment. More...

  • Biomolecule-small molecule labelings
  • Biomolecule-biomolecule conjugations
  • Immobilization on solid supports

Antisense Oligonucleotides

Use antisense oligonucleotides for your gene silencing experiments. We hybrid designs using various types of nucleotide analogs to increase high affinity for a successful knockdown experiments. More....

  • Phosphorothioate oligos
  • Constrained ribose (ENA, ZNA)
  • 2' OMethyl Base
  • 2' Fluoro RNA
  • Peptide Nucleic Acids (PNA)
  • Peptide Nucleic Acids (PNA)
  • Morpholino
  • 5-Me-dC
  • Propyne dC or dU

Black Hole QuencherTM IQ4 Quencher (Alternative of BHQ1,2,3)
Eclipse@ Dakr Quencher -

Fluorophore Labelings
Alexa Fluor® Dyes Epoch Dye and Quencher
ATTO-TEC Dyes Fluorescein Dye
Bodipy® Fluorophores Oregon Green
Cyanine Dye Other Molecular Probe Dyes
Dyomic Dyes Oyster Dye
Rhodamine Dyes DyLight Dyes

Redox Labels

Bio-Synthesis offers labeling of oligonucleotide or peptide/protein with redox active compounds for electrochemical studies.

  • Dicarboxymethylene Blue
  • Monocarboxymethylene Blue
  • Ferrocene, Ferrocene-C6
  • Anthraquinone, Anthraquinone-C6

Metal Chelates

Bio-Synthesis offers metal chelator oligo incorporation of 2,2’-Dipicolylamine. This is a versatile metal-coordinating ligand capable of forming complexes with common metal ions including Zn2+, Ni2+, Cu2+, or Ag+. A tremendous advantage of dipicolylamine is complete compatibility with standard DNA synthesis, cleavage and purification protocols. Other chelating ligands may require nonstandard conditions or additional protection and deprotection steps. This product was manufactured and developed by Syntrix Biosystems Inc. Patents Pending. For Research Use Only.

Polyaromatic Hydrocarbons Labelings

Pyrene and perylene are fluorescent polycyclic aromatic hydrocarbons that have the ability to form ‘excited state dimers’ known as excimers. This unstructured, long-wavelength emission arises from the formation of a charge-transfer complex between the excited state and the ground state of two fluorescent molecules. In Pyrene-dU and perylene-dU, the hydrocarbon is attached at the 5 position of deoxyuridine through a triple bond and is electronically coupled to the deoxyuridine base. This electronic coupling of the base and the hydrocarbon makes the fluorescence sensitive to the base pairing of the dU portion of the molecule, allowing the discrimination between perfect and one base mismatched targets.

  • Pyrene-dU
  • Perylene-dU

Photo Regulation Oligo Labelings

Photo-control, the use of ultraviolet or visible light to control a reaction, has a number of advantages over other external stimuli:

  • Light does not introduce contaminants into the reaction system
  • Excitation wavelength can be controlled through the design of the photo-responsive molecule
  • Controling irradiation time and/or local excitation is now straightforward

When a photo-responsive molecule is directly attached to DNA as a receptor, photo-regulation of the bioprocess regulated by that DNA molecule could, in principle, be achieved. Such photo-responsive DNA could also be used as a switch in a DNA-based nano-machine. Professor Hiroyuki Asanuma and his group at the department of Molecular Design and Engineering of the Graduate School of Engineering of the Nagoya University (Japan) have developed an efficient method to achieve this goal. They have attached azobenzene to DNA and made it photo-responsive. Azobenzene is a typical photo-responsive molecule that isomerizes from its planar trans-form to the non-planar cis-form after UV-light irradiation with a wavelength between 300 nm and 400 nm (lmax is around 330 nm). Interestingly, the system reverts from the cis-form to the trans-form after further irradiation with visible light (wavelength over 400 nm). This process is completely reversible, and the azobenzene group does not decompose or induce undesirable side reactions even on repeated trans-cis isomerization. By introducing azobenzenes into DNA through D-threoninol as a linker, Asanuma and co-workers succeeded in achieving photo-regulation of:

  • Formation and dissociation of a DNA duplex.
  • Transcription by T7-RNA polymerase reaction.

Fluorogenic Probes and Primers for Real-time qPCR
Labeled Probes Amplifluor Direct® Primers
Molecular Beacons for Gene Detection and Analysis Plexor™ Primers
Black Hole Scorpion™ Primers

Probes for Multiplexing qPCR
Labeled Probes Amplifluor Direct® Primers
Molecular Beacon Black Hole Scorpions™ Probe, Uni-molecular

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Disclaimer: FAMTM, HEXTM, ROXTM, TAMRATM and TETTM are trademarks of Applied Biosystems, Inc. CyTM is a trademark of GE Healthcare; Texas RedTM is a trademark of Molecular Probes Eclipse® and Yakima Yellow® are registered trademarks of Epoch Biosiences, Inc. BHQ 1TM and BHQ 2TM are trademarks of Biosearch Technologies, Inc. BlackBerry (BBQ)TM is a trademark of Berry & Associates, Inc. LightCycler® probes are sold under the license from Roche Diagnostics Gmbh