AAT Bioquest

CDPI3 Alkyne [Minor Groove Binder Alkyne]

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Physical properties
Molecular weight1403.64
Storage, safety and handling
H-phraseH303, H313, H333
Hazard symbolXN
Intended useResearch Use Only (RUO)
R-phraseR20, R21, R22
StorageFreeze (< -15 °C); Minimize light exposure


Molecular weight
Minor Groove Binder (MGB) molecules selectively bind to the minor groove of a DNA molecule, the shallow furrow in the DNA helix. MGB-labeled oligonucleotides form stable hybrid complexes with complementary DNA and RNA target sequences. Dihydropyrroloindole tripeptide (CDPI3), the analogs of natural product CC-1065, have been shown to arrest sequence-specific primer extension on single-stranded DNA when linked to oligonucleotides. CDPI3-containing oligonucleotides increases both the specificity and the strength of hybridization, thus enhancing the stability of DNA duplexes. The addition of MGB molecules to DNA probes allows the design of shorter hybridization probes useful for molecular diagnostics, e.g., quantitative PCR based assays. Several designs are possible, including Taqman MGB probes. Compared to other commercial MGB probes, AAT Bioquest offer this MGB building block that contains a methylpiperazine moiety (derived from Hoechst 33258, another popular MGB molecule) to further enhance its DNA affinity. We offer CDPI3 alkyne for labeling azide-modified oligos.


Common stock solution preparation

Table 1. Volume of DMSO needed to reconstitute specific mass of CDPI3 Alkyne [Minor Groove Binder Alkyne] to given concentration. Note that volume is only for preparing stock solution. Refer to sample experimental protocol for appropriate experimental/physiological buffers.

0.1 mg0.5 mg1 mg5 mg10 mg
1 mM71.243 µL356.217 µL712.433 µL3.562 mL7.124 mL
5 mM14.249 µL71.243 µL142.487 µL712.433 µL1.425 mL
10 mM7.124 µL35.622 µL71.243 µL356.217 µL712.433 µL

Molarity calculator

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