Synthetic oligonucleotides with covalently-attached CDPI3 have enhanced DNA affinity and 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. 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-(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
6-(6-(Ethoxycarbonyl)-7-(6-(ethoxycarbonyl)-7-(6-(ethoxycarbonyl)-7-(methyl(6-(2,2,2-trifluoro-N-methylacetamido)hexyl)carbamoyl)-1,2,3,6-tetrahydropyrrolo[3,2-e]indole-3-carbonyl)-1,2,3,6-tetrahydropyrrolo[3,2-e]indole-3-carbonyl)-1,2-dihydropyrrolo[3,2-e]indol-3(6H)-yl)-6-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite