5'-CDPI3 MGB™ Phosphoramidite


Product Specifications

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The tripeptide of dihydropyrroloindole-carboxylate (CDPI3) is a minor groove binding (MGB) moiety derived from the natural product CC-1065 with strong DNA binding properties. Synthetic oligonucleotides with covalently-attached CDPI3 have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. Short CDPI3-oligonucleotides hybridize with single-stranded DNA to give more stable DNA duplexes than unmodified ODNs of similar length. CDPI3MGβ-oligonucleotide conjugates have been found to be useful in the following applications:

  • Arrest of primer extension and PCR blockers
  • Short and fluorogenic PCR primers
  • Real-time PCR probes
  • miRNA Inhibitors

The simplest approach to MGB probe design is to use an MGB support, add a quencher molecule as the first addition and complete the synthesis with a 5'-fluorophore. Alternatively, a fluorophore support could be used with the 5' terminus containing a quencher molecule followed by a final MGB addition at the 5' terminus. Glen Research offers 5'-CDPI3 MGB™ Phosphoramidite and 3'-CDPI3

MGB™ CPG. 5'-CDPI3 MGB phosphoramidite was found to be hydrophobic enough that it required 10% THF in ACN to go completely into solution at a 0.1 M concentration and required a 3 minute coupling time. Deprotection can be carried out in EtOH/NH4OH 1:3 (v/v) 17 hr at 55°C and CDPI3 MGBis compatible with GlenPak™ purification.

With the CDPI3 MGB CPG, the optimal results are obtained if UltraMild monomers and Cap A are used during synthesis along with 0.5 M CSO oxidizer. However, the use of standard monomers with iodine oxidation followed by deprotection with EtOH/NH4OH 1:3 (v/v) for 17 hr at 55 °C will give acceptable results.



  • Coupling: 3 minute coupling time recommended.
  • Deprotection: 30% Ammonium Hydroxide/Ethanol 3:1 (v/v) for 17 hours at 55�C
Diluent 10% THF in Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°C, dry
Stability 1-2 Days

Intellectual Property

Yakima Yellow®, Redmond Red®, Eclipse® and MGB Eclipse® are registered Trademarks of ELITechGroup. Product is made and sold under license from ELITechGroup.

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-5924-02 0.25 g .25grams 1.89 49.67 29.8 18.63 13.55 9.93 2.48
10-5924-90 100 µmol .132grams 1 20 12 7.5 5.45 4 1
10-5924-95 50 µmol .066grams 0.5 3.33 2 1.25 0.91 0.67 0.17


Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-5924-02 0.25 g .25grams 2.82 0.07 50 31.25 22.73 3.13
10-5924-90 100 µmol .132grams 1.5 0.07 23.6 14.75 10.73 1.48
10-5924-95 50 µmol .066grams 0.75 0.07 8.6 5.38 3.91 0.54