AAT Bioquest

CDPI3 Succinimidyl Ester [Minor Groove Binder SE]

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InternationalSee distributors
ShippingStandard overnight for United States, inquire for international
Physical properties
Molecular weight1463.65
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 succinimidyl ester for labeling amino-modified oligos.


Common stock solution preparation

Table 1. Volume of DMSO needed to reconstitute specific mass of CDPI3 Succinimidyl Ester [Minor Groove Binder SE] 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 mM68.322 µL341.612 µL683.223 µL3.416 mL6.832 mL
5 mM13.664 µL68.322 µL136.645 µL683.223 µL1.366 mL
10 mM6.832 µL34.161 µL68.322 µL341.612 µL683.223 µL

Molarity calculator

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View all 31 references: Citation Explorer
Carbocyclic Analogues of Distamycin and Netropsin.
Authors: Arciszewska, Karolina and Pućkowska, Anna and Wróbel, Agnieszka and Drozdowska, Danuta
Journal: Mini reviews in medicinal chemistry (2019): 98-113
Synthesis of a novel 4H-pyran analog as minor groove binder to DNA using ethidium bromide as fluorescence probe.
Authors: Ramana, M M V and Betkar, Rahul and Nimkar, Amey and Ranade, Prasanna and Mundhe, Balaji and Pardeshi, Sachin
Journal: Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy (2016): 165-71
Quantitation of substitutions at amino acid 70 in hepatitis C virus genotype 1b.
Authors: Hu, Zhongjie and Liu, Ying and Qiu, Lixia and Fan, Zuopeng and Nie, Wei and Liang, Shan and Jin, Ronghua
Journal: Virology journal (2014): 148
Multi-spectroscopic and molecular modeling studies on the interaction of antihypertensive drug; methyldopa with calf thymus DNA.
Authors: Shahabadi, Nahid and Maghsudi, Maryam
Journal: Molecular bioSystems (2014): 338-47
Classification of DNA minor and major grooves binding proteins according to the NLSs by data analysis methods.
Authors: Amanzadeh, Elnaz and Mohabatkar, Hassan and Biria, Davoud
Journal: Applied biochemistry and biotechnology (2014): 437-51
Antiprotozoal activity and DNA binding of N-substituted N-phenylbenzamide and 1,3-diphenylurea bisguanidines.
Authors: Ríos Martínez, Carlos H and Lagartera, Laura and Kaiser, Marcel and Dardonville, Christophe
Journal: European journal of medicinal chemistry (2014): 481-91
Minor groove binders as anti-infective agents.
Authors: Barrett, Michael P and Gemmell, Curtis G and Suckling, Colin J
Journal: Pharmacology & therapeutics (2013): 12-23
Weight loss effects of quaternary salts of 5-amino-1-(chloromethyl)-1,2-dihydro-3H-benz[e]indoles; structure-activity relationships.
Authors: Tercel, Moana and Stevenson, Ralph J and Lu, Guo-Liang and Stribbling, Stephen M and Wilson, William R and Tatnell, Michele A and Marnane, Rebecca N and Mountjoy, Kathleen G and Denny, William A
Journal: Bioorganic & medicinal chemistry (2012): 734-49
Characterization of Canine parvovirus 2 variants circulating in Greece.
Authors: Ntafis, Vasileios and Xylouri, Eftychia and Kalli, Iris and Desario, Costantina and Mari, Viviana and Decaro, Nicola and Buonavoglia, Canio
Journal: Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagn (2010): 737-40
[Design, synthesis and evaluation of polyamide-nucleoside hybrids and oligonucleotides conjugated hybrid as a novel gene expression control compound].
Authors: Kawashima, Etsuko and Kamaike, Kazuo
Journal: Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan (2010): 355-75