Intercalation of small molecules into DNA is photochemically achieved by in situ irradiation of a tetraaryl-pyridinium species. Such a "DNA intercalation on demand" process could highlight an alternative pathway to anticancer basic research, based on photo-activable DNA binders.

YOYO-1 is a green fluorescent dye which is widely used to image single DNA molecules in solution for biophysical studies. However, the question of whether the intercalation of YOYO-1 affects the mechanical properties of DNA is still not clearly answered. Investigators have put forth contradicting data on the changes in persistence length of DNA. Here, we use atomic force microscopy to systemati...

A highly oriented film was fabricated by layer-by-layer self-assembly of DNA and MgAl-layered double hydroxide nanosheets, and its application in chiroptical switch was demonstrated via intercalation and deintercalation of an achiral molecule into the DNA cavity. DNA molecules are prone to forming an ordered and dispersive state in the interlayer region of rigid layered double hydroxide (LDH) n...

In this work the data of methylene blue (MB) and Hoechst 33258 interaction with DNA are presented. It has been shown that at 0.002 M ionic strength of solution MB is bound to double-stranded DNA by three modes: intercalation, semi-intercalation and electrostatic. It was revealed that at higher ionic strengths of solution complete intercalation of MB becomes thermodynamically unacceptable. It wa...

The mechanism of intercalation and the ability of double stranded DNA (dsDNA) to accommodate a variety of ligands in this manner has been well studied. Proposed mechanistic steps along this pathway for the classical intercalator ethidium have been discussed in the literature. Some previous studies indicate that the creation of an intercalation site may occur spontaneously, with the energy for t...

Semiempirical CNDO/2 calculations of the electronic and molecular structures have been carried out for six antitumor anthracycline antibiotics. The strong correlation between their biological activity and such molecular properties as chromophore dipole moment, energy of frontier orbitals, and steric volumes was found and the proper QSAR equations were constructed. The molecular mechanics model ...

We measured the effect of the intercalating oxazole yellow DNA dye quinolinium,4-[(3-methyl-2(3H)-benzoxazolylidene)methyl]-1-[3-(trimethylammonio)propyl]-,diiodide (YO-PRO) and its homodimer (YOYO) on the melting of self-complementary DNA duplexes using a gel-based assay. The assay, which requires a self-complementary DNA sequence, is independent of the optical properties of the molecules in s...

Nucleotide flipping is a common feature of DNA-modifying enzymes that allows access to target sites within duplex DNA. Structural studies have identified many intercalating amino acid side chains in a wide variety of enzymes, but the functional contribution of these intercalating residues is poorly understood. We used site-directed mutagenesis and transient kinetic approaches to dissect the ene...