Competitive DNA-Binding Studies between Metal Complexes and GelRed as a New and Safe Fluorescent DNA Dye

Abstract

The focus of this work is introduction of GelRed (GR) as a stable, sensitive and environmentally safe fluorescent DNA dye instead of the highly toxic ethidium bromide (EB). Competitive DNA-binding studies between metal complexes, [Cu(phen-dion)(phen)Cl]Cl (1), [Cu(phen-dione)(bpy)Cl]Cl (2), [Cu(dppt)2(H2O)]PF6 (3), [Ni(dppt)2Cl2] (4), [Zn(dppt)2Cl2] (5), and K3[Fe(CN)6] (6) (where phen-dione is 1,10-phenanthroline-5,6-dione, phen is 1,10- phenanthroline, bpy is 2,2'-bipyridine, and dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), and GelRed have been investigated under physiological conditions by fluorescence spectroscopy. This simple method can reveal the binding affinity and mode of metal complexes with DNA. The method is based on the decrease of fluorescence derived from the displacement of GelRed from DNA by metal complexes. The % fluorescence decrease is directly related to the extent of DNA binding. Results indicate the DNA binding affinities of complexes follow the order 3 > 4 > 1 > 2 > 5 > 6. The significant quenching of the emission band of the GR-DNA with the addition of complexes 1, 3, and 4 suggests that complexes compete for DNA-binding sites with GR and displace GR from the GR-DNA, which is usually characteristic of the intercalative interaction of compounds with DNA. A small quenching of the emission band of the GR-DNA with the addition of the complex 2 was observed that show the complex weaker competes for DNA-binding sites with GR than complexes 1, 3, and 4. Results show complexes 5 and 6 cannot compete for DNA-binding sites with GR and their interaction with DNA is external binding (groove or electrostatic bindig).

Competitive Binding of Novel Cyanine Dye AK3-5 and Europium Coordination Complexes to DNA

“…The most probable explanation for this observation is the different binding affinities of the europium complexes. Similarly, the metal complexes of Cu, Zn and Ni have been reported to possess the distinct DNA binding affinities [5]. Interestingly, V5 and V10 are more bulky in comparison to V7 and V9.…”

“…The above dependencies were analyzed in terms of the simplified competition model (Eqs. [2][3][4][5][6][7][8][9][10][11][12][13] to calculate the association constants of the drug ( drug K ) binding to the DNA in the presence of AK3-5. The calculated drug K values were equal to 5.4×10 4 M -1 and 3.9×10 5 M -1 for V7 and V9, respectively.…”

“…Due to advantages of rapidity and sensitivity, the fluorescence drug displacement assay seems to be an especially promising for the investigation of mechanisms underlying the interaction between nucleic acids and drugs. This method is based on a strong enhancement in the dye emission upon its binding to DNA or RNA, followed by the fluorescence drop upon the dye displacement by the drug [4][5][6][7]. Among a variety of commercially available dyes, ethidium bromide is the most widely used in the displacement experiments [7,8].…”

Immunoassay-aptasensor for the determination of tumor-derived exosomes based on the combination of magnetic nanoparticles and hybridization chain reaction

“…In this work, we used the exosomes triggering the HCR and obtained the super-long dsDNA. The GelRed, being a stable, sensitive and environmentally friendly uorescent nucleic acid staining dye, 31,32 could chimerize into the dsDNA structure and generate a strong uorescence signal. 33 Thus, we could realize the detection of tumor-related exosomes by measuring the nal uorescence signal.…”

A New Samarium(III) Complex of Liriodenine: Synthesis, Crystal Structure, Antitumor Activity, and DNA Binding Study

“…The fluorescence intensity of GR is very weak in aqueous solution, but it will enhance when existed in the hydrophobic circumstance, such as between the adjacent base pairs of DNA. It is generally regarded that the strong emission of the GR‐DNA complex can be effectively reduced if a DNA intercalator competitively binds with the GR‐DNA binary system, so that it has been used as a simple method to examine the binding affinity and binding mode of the metal complexes with DNA , …”