Study of the DNA/ethidium bromide interactions on mica surface by atomic force microscope: Influence of the surface friction

Abstract

The influence of mica surface on DNA/ethidium bromide interactions is investigated by atomic force microscopy (AFM). We describe the diffusion mechanism of a DNA molecule on a mica surface by using a simple analytical model. It appears that the DNA diffusion on a mica surface is limited by the surface friction due to the counterion correlations between the divalent counterions condensed on both mica and DNA surfaces. We also study the structural changes of linear DNA adsorbed on mica upon ethidium bromide binding by AFM. It turns out that linear DNA molecules adsorbed on a mica surface are unable to relieve the topological constraint upon ethidium bromide binding. In particular, strongly adsorbed molecules tend to be highly entangled, while loosely bound DNA molecules appear more extended with very few crossovers. Adsorbed DNA molecules cannot move freely on the surface because of the surface friction. Therefore, the topological constraint increases due to the ethidium bromide binding. Moreover, we show that ethidium bromide has a lower affinity for strongly bound molecules due to the topological constraint induced by the surface friction.

Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

“…In a second study 40 , the surface diffusion rate of the same 1.4 knt dsDNA was related to electrostatic surface friction, which was in turn related to the strength of ion correlations. Ni 2 þ -treatment of mica prevented geometric rearrangement of highly entangled DNA, which otherwise was able to untangle.…”

“…Ni 2 þ apparently binds to mica so strongly that Ni 2 þ pretreatment of the surface is all that is necessary to immobilize short dsDNA 31,40 . The idiosyncratic properties of each divalent metal cation with respect to DNA binding to mica have been partially attributed to cationic radius or enthalpies of hydration 29 or specific complexation of the ions with DNA or mica 31 , but no theory consistently explaining the behaviour of all divalent cations seems to exist.…”

“…Further complicating matters, monovalent cations commonly present in buffer solutions such as Na þ , K þ or TrisH þ can decrease the interaction of divalent cations with DNA and mica. 31,32,35,36 For particular cations, for linear dsDNA, three studies by the same group have been successful in explaining strong-to-weak binding transitions of particular relevance to our system 31,32,40 .…”

The influence of GC/AT composition on intercalating and semi-intercalating binding of ethidium bromide to DNA

“…[1][2][3][4][5][6][7] Majority of intercalators might form more than one type of complexes with DNA (multimodal ligands), the prominent representative of which is ethidium bromide (EtBr). Investigations showed that at small values of drug/DNA ratio (r) this ligand may form two types of "strong" complexes with DNA, one of which has been proposed to be a stably bound external binding and second type is the well described intercalation mode.…”

Experimental and theoretical investigation effect of flavonols antioxidants on DNA damage

“…This compound can further oxidative damage to DNA in cancerous cells through the generation of reactive oxygen species [20]. AO bind DNA via intercalative manner and slip between next base pairs and stabilizes pigment-DNA complexes through charge neutralization of DNA backbone phosphate group [21], which cause stretch of double helical structure [22][23][24]. Moreover, the M A N U S C R I P T…”