DNA aggregation induced by Mg²⁺ ions under different conditions

Abstract

Cations-induced DNA aggregation can modify the local structure of oligonucleotides and has potential applications in medicine and biotechnology. Here, we used atomic force microscopy to investigate λ-DNA aggregation on Mg -treated glass (Mg /glass) and in Mg solution. Atomic force microscopy topography images showed that some DNA fragments were slightly stacked together on 10 mM Mg /glass and stacked stronger on ≥50 mM Mg /glass. They also showed that DNA aggregated stronger in Mg solution than on Mg /glass, ie, DNAs are strongly stacked and twisted at 10 mM Mg , rolled together at 50 mM Mg , and slightly aggregated to form small particles at 100 mM Mg . At a specific condition, ie, heating λ-DNA to 92°C, cooling down to 75°C, adding Mg , and vortexing the resulting solution, DNA strongly aggregated and formed pancake-like shapes at 10 and 50 mM or a large aggregate at 100 mM Mg solutions. Our results may be helpful for medical applications and gene therapy using cation-DNA technology.

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D

“…It is involved in more than 600 enzymatic reactions and plays a crucial role in vital processes such as ATP hydrolysis, cellular signaling, or the catalytic activity of ribozymes . The specific requirement for Mg 2+ is prevalent in nucleic acid systems where Mg 2+ is crucial for the stability, folding, and biological function. − In addition to its physiological relevance, Mg 2+ is important in DNA nanotechnology − and is a promising candidate for divalent batteries. , …”

Investigation of the Presence of DNA in Human Blood Plasma Small Extracellular Vesicles

“…Exosomes released from astrocytes, glioblastoma cells, prostate cancer cells, reticulocytes, dendritic cells or melanoma cells contain phosphatidylinositol [ 27 , 28 , 29 ]; therefore, we propose that the interactions of histones with phosphatidylinositol could contribute to the aggregation of sEVs. Mg 2+ cations could also be responsible for the aggregation and changes in shape of DNA, as the aggregation of DNA molecules occurred at higher concentrations of Mg 2+ in the solution [ 30 ], which is also important to stress since blood was collected into heparin tubes in our case. Our measurements show that it is probably more appropriate to use DNase before the UC, which potentially prevents the formation of aggregates, and this, in turn, changes the size distribution profile according to our data.…”

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

“…The interactions of DNA with metal ions and small molecules facilitate fundamental cellular processes [ 139 , 140 , 141 , 142 ] such as genomic stability [ 139 , 143 , 144 , 145 , 146 , 147 ], DNA-carcinogen interactions [ 146 , 147 , 148 , 149 , 150 , 151 ], drug development [ 152 , 153 , 154 , 155 ], and DNA-based metal-biosensors [ 156 ]. As mentioned earlier, the rigidity of DNA is affected by the type and concentration of metal ions.…”