CDPI3 MGB™ Labeling of Oligonucleotides

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. CDPI3 MGB-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 MGB is compatible with GlenPak™ purification.

With the CDPI3 MGB CPG, 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.

Legal Notice

NOTICE TO PURCHASER: 

LIMITED LICENSE 

This product is sold under licensing arrangements between ELITechGroup Inc. and Glen Research.  The purchase price of this product includes limited, nontransferable rights to use the product solely for activities of the purchaser which are directly related to human diagnostics.  Other uses, including incorporation of the product into another commercial product, are prohibited without additional license rights.  For information on purchasing a license to this product for purposes other than those stated above, contact: 

ELITech Group Molecular Diagnostics

21720 23rd Drive SE, Suite 150 

Bothell, WA 98021  

Phone (425) 482-5555  

Fax (425) 482-5550 

Email: [email protected]

This limited license permits the person or legal entity to which this product has been provided to use the product, and the data generated by use of the product, only for human diagnostics.  Neither ELITechGroup Inc. nor its licensors grants any other licenses, expressed or implied for any other purposes.

Some components of nucleic acid analysis, such as specific methods and compositions for manipulating or visualizing nucleic acids for analysis, may be covered by one or more patents owned by other parties.  Similarly, nucleic acids containing specific nucleotide sequences may be patented.  Making, using, offering for sale, or selling such components or nucleic acids may require one or more licenses.  Nothing in this document should be construed as an authorization or implicit license to make, use or sell any so covered component or nucleic acid under any such patents.