Crowding by Anionic Nanoparticles Causes DNA Double-Strand Instability and Compaction

Abstract

Up to the present, DNA structural transitions caused by cationic polymers as well as in concentrated solutions of neutral polymers are well documented, while a little is known about DNA interaction with like-charge species. Herein, changes in the structure of DNA induced by anionic nanoparticles of different sizes (20-130 nm) were investigated by combining single-molecule DNA fluorescent microscopy, to monitor the conformational dynamics of long-chain DNA, with spectroscopic methods, to gain insight into changes in the secondary structure of DNA. The results showed that several percent of negatively charged silica nanoparticles induced DNA compaction from a coil to a globule, and this change was accompanied by a decrease in the melting temperature of the DNA double helix. DNA was compacted into toroidal condensates with reduced diameters of about 20-30 nm. Smaller 20 nm nanoparticles triggered a DNA coil-globule transition at lower concentrations, but the exclusion volume for each type of nanoparticle at the point of complete DNA collapse, as estimated by taking into account the depth of the ionic atmosphere, was found to be almost the same.

Compaction of bacterial genomic DNA: clarifying the concepts

“…It is seen in this figure that, at 1% BSA and 150 mM NaCl, the 166 kbp bacteriophage T4 DNA exhibits an elongated coil conformation, which is approximately 5 µm long (figure 4(A)), while at 15% BSA the DNA is tightly between these macromolecules and leads eventually to re-mixing. Note that it was still more recently shown that a few percents of negatively charged silica nanoparticles with diameters ranging from 20 to 135 nm are also able to trigger compaction of DNA from coil to globule configurations [45].…”

A Green Solvent Induced DNA Package

“…Moreover, mechanically compacted DNA has recently been used as nanostructure template4 and also applied as protection against chemical, biochemical and mechanical stresses5. Learning from the nature, researchers have started applying the compaction tricks using polyamines67, surfactants89, liposomes10, nanoparticles1112, polymer13, osmoticants like polyethylene glycol (PEG)14, dendrimers1516, multivalent ions17, metal complex18, cyclodextrin19, peptides20 and proteins21 for compaction and storage of DNA for prolonged duration. Among these compacting agents, most important naturally occurring DNA compaction agents are proteins and polyamines like of spermine and spermidine etc2021.…”

Compaction of double-stranded DNA by negatively charged proteins and colloids

“…In contrast to the destabilization of DNA secondary structure observed by Zinchenko et al [29], Liu et al reported a significant increase of DNA melting temperature in solutions containing high concentrations of polyanion. At a similar ionic strength (2.5 mM Na + ) they measured an increase in the melting temperature of 12 bp DNA from 38°C to 50°C by just adding 1% PAANa to solution.…”

“…2 top) [29]. To avoid aggregation of nanoparticles, the experiments were performed at low salt concentrations (1 mM NaCl).…”

“…Compaction of DNA in solutions of neutral polymers often leads to the folding of DNA into compact particles with a toroidal morphology and 50-100 nm size [31,32]. Transmission electron microscopy observations in [29] revealed that DNA toroids formed in solutions of anionic nanoparticles are significantly smaller, around 20-30 nm. Formation of the DNA toroids with reduced dimensions is ascribed to the decrease of DNA rigidity as a result of partial denaturation (melting) in solutions of anionic crowder.…”