Ligand–DNA interaction in a nanocage of reverse micelle

Abstract

We have studied intercalation of ethidium bromide (EB) to genomic DNA encapsulated in a nanospace of an anionic AOT reverse micelle (RM). Circular dichroism (CD) study on the DNA in the RM reveals its condensed form. Here, we have used temporal decay-associated spectra (DAS) and time-resolved area normalized emission spectral (TRANES) techniques to investigate EB-binding to condensed DNA because the interference of emission from unbound EB in the RM makes conventional steady state and picosecond resolved fluorescence spectroscopic techniques challenging. The binding affinity of the ligand EB with the DNA in the RM is found to increase with the size of the RM, reflecting the effect of lessening of DNA condensation on the binding affinity. CD spectra of the DNA in the RM with various sizes indicate the structural change of the condensed DNA with reverse micellar size. DAS and TRANES techniques along with dynamic light scattering studies of the EB-DNA complex in the RM further reveal two kinds of binding modes of the ligand with the condensed DNA even in essentially monodispersed RMs. To investigate the role of RM on the ligand binding and secondary structure of the DNA, we have also studied complexation of EB with two synthetic self-complimentary oligonucleotides of sequences (CGCAAATTTGCG)2 and (CGCGCGCGCGCG)2 in the RM.

Slow Solvent Relaxation Dynamics of Nanometer Sized Reverse Micellar Systems Through Tryptophan Metabolite, Kynurenine

“…The C ( t ) function represents the temporal response of the solvent relaxation process, as occurs around the probe following its photoexcitation and the associated change in the dipole moment. To ascertain the heterogeneity in the location of KN in the RM, we further followed the time‐resolved area normalized emission spectral (TRANES) technique (14,15). TRANES is a model‐free modified version of TRES mentioned earlier.…”

“…To ascertain the heterogeneity in the location of KN in the RM, we further followed the time-resolved area normalized emission spectral (TRANES) technique (14,15). TRANES is a model-free modified version of TRES mentioned earlier.…”

Dynamical perspective of protein-DNA interaction

“…From Table 1, it is evident that the faster time constant ( < 3.5 ns) of EtBr in the duplex2 without H1 is slower than that in buffer (1.5 ns) and much faster than that of the DNA-bound EtBr through intercalative interaction (22 ns). The time constant may indicate that EtBr molecules are loosely bound to the DNA through nonintercalative interaction, namely electrostatic binding (40). However, in the duplex2-H1 complex, the loosely bound EtBr molecules are detached and show a time constant of 1.8 ns similar to that in the bulk buffer (1.5 ns).…”

Synthesis, pH-induced “on–off–on” luminescence switching, and partially intercalative DNA-binding and DNA photocleavage properties of an β-d-allopyranoside-grafted ruthenium(II) complex

“…An intercalative complex can usually almost fully displace EB from DNA-bound EB, and the fluorescence of EB-DNA solution will be quenched due to the fact that free EB molecules are readily quenched by the surrounding water molecules [65,66]. Previous reports indicated that EB has two DNA binding modes, primarily intercalatively and partially groove bound to the DNA [67][68][69][70][71]. EB was also reported to intercalate into DNA through interactions with the minor groove of the DNA, the displacement of EB by the titration of a drug is thus suggestive of an intercalative or minor groove binding.…”