CDPI3 MGB™ CPG

5-(6-(6-(6-(6-Dimethoxytrityloxyhexanoyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carbonyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carbonyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carboxamido)pentyl-1-O-diglycoloyl long chain alkylamino CPG

Product Specifications

F.W.:
831.87
Pore Size:
1000Å
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Description

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.

Details

Usage

  • Coupling: Regular with UltraMild monomers and Cap A (Catalog Numbers: dA: 10-1601-xx, dC: 10-1015-xx, dG: 10-1621-xx, dT: 10-1030-xx and Cap A 40-4210-xx/40-4212-xx). Use 0.5 M CSO in ACN for oxidation (Catalog Number 40-4632-xx) using a 3 minute oxidation time.
  • Deprotection: Cleave and deprotect the oligonucleotide in 30% Ammonium Hydroxide for 2 hours at Room Temperature. If standard monomers and iodine oxidation are used, acceptable results can be obtained when deprotected in NH4OH/EtOH 3:1 (v/v) for 17 hr at 55°C.
Specifications
Storage Refrigerated storage, maximum of 2-8°C, dry

Intellectual Property

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