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SML2298

Sigma-Aldrich

PhenDC3

≥97% (HPLC), powder, G-quadruplex ligand

Synonym(s):

3,3′-[1,10-Phenanthroline-2,9-diylbis(carbonylimino)]bis[1-methylquinolinium] 1,1,1-trifluoromethanesulfonate (1:2), Phen DC3, Phen-DC(3), Phen-DC3

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About This Item

Empirical Formula (Hill Notation):
C34H26N6O2 · 2CF3SO3
CAS Number:
929895-45-4
Molecular Weight:
848.75
UNSPSC Code:
12352200
NACRES:
NA.77

product name

PhenDC3, ≥97% (HPLC)

Assay

≥97% (HPLC)

form

powder

color

white to beige

solubility

DMSO: 2 mg/mL, clear

storage temp.

2-8°C

SMILES string

O=C(NC1=CC2=CC=CC=C2[N+](C)=C1)C3=CC=C4C=CC5=CC=C(N=C5C4=N3)C(NC6=CC7=CC=CC=C7[N+](C)=C6)=O.O=S([O-])(C(F)(F)F)=O.O=S([O-])(C(F)(F)F)=O

Application

PhenDC3 has been used:
  • as a quadruplex (G4) ligand to study its effects on the binding of RNA quadruplex (rG4) to nucleolin (NCL)
  • as a DNA/RNA G-quadruplexes (GQs) ligand to study its effects on the expression of double homeobox 4 (DUX4) gene
  • as a G4 ligand to study its stability and selectivity towards pre-miR-92b rG4 complex and duplex DNA by fluorescence resonance energy transfer (FRET)-melting assay

Biochem/physiol Actions

PhenDC3 (Phen-DC3) is a bisquinolinium-derivatized phenanthroline-dicarboxamide that targets both DNA and RNA G-quadruplex (G4) structure with high affinity (DNA DC50 in μM = 0.31/22AG K+, 0.25/22AG Na+, 0.30/TBA; RNA DC50 in μM = 0.11/(G3U)3G3, 0.12/(G3U2)3G3, 0.16/(G3U3)3G3) and selectivity (duplex DNA DC50 >2.5 μM). PhenDC3 suppresses the translation of reporter mRNA constructs with 5′UTR G4 structure, but not those without, in cell-based reporter assays (0.1-10 μM) and reduces telomerase processivity by promoting telomerase dissociation from its product during elongation. NMR analysis shows that PhenDC3 interacts with the quadruplex through extensive stacking with the guanine bases of the top G-quartet. A powerful benchmark tool for probing and elucidating the biological roles of cellular DNA and RNA G4 sturctures.

Storage Class Code

11 - Combustible Solids

WGK

WGK 3

Flash Point(F)

Not applicable

Flash Point(C)

Not applicable

Certificates of Analysis (COA)

Search for Certificates of Analysis (COA) by entering the products Lot/Batch Number. Lot and Batch Numbers can be found on a product’s label following the words ‘Lot’ or ‘Batch’.

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Kevin Kok-Phen Yan et al.
Nucleic acids research, 49(14), 8339-8354 (2021-07-25)
The identification of G-quadruplex (G4) binding proteins and insights into their mechanism of action are important for understanding the regulatory functions of G4 structures. Here, we performed an unbiased affinity-purification assay coupled with mass spectrometry and identified 30 putative G4
Judith Lopes et al.
The EMBO journal, 30(19), 4033-4046 (2011-08-30)
G-quadruplexes are four-stranded nucleic acid structures whose biological functions remain poorly understood. In the yeast S. cerevisiae, we report that G-quadruplexes form and, if not properly processed, pose a specific challenge to replication. We show that the G-quadruplex-prone CEB1 tandem
Efficient suppression of gene expression by targeting 5'-UTR-based RNA quadruplexes with bisquinolinium compounds.
Kangkan Halder et al.
Chembiochem : a European journal of chemical biology, 12(11), 1663-1668 (2011-06-18)
Aurèle Piazza et al.
Nucleic acids research, 38(13), 4337-4348 (2010-03-13)
G-quadruplexes are nucleic acid secondary structures for which many biological roles have been proposed but whose existence in vivo has remained elusive. To assess their formation, highly specific G-quadruplex ligands are needed. Here, we tested Phen-DC(3) and Phen-DC(6), two recently
Aleksandr B Sahakyan et al.
Nature structural & molecular biology, 24(3), 243-247 (2017-01-31)
Long interspersed nuclear elements (LINEs) are ubiquitous transposable elements in higher eukaryotes that have a significant role in shaping genomes, owing to their abundance. Here we report that guanine-rich sequences in the 3' untranslated regions (UTRs) of hominoid-specific LINE-1 elements
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