Salt Induced Structural Collapse, Swelling, and Signature of Aggregation of Two ssDNA Strands: Insights from Molecular Dynamics Simulation

Abstract

Molecular dynamics simulations elucidate the structural collapse shown by two ssDNAs of the same base sequence in the presence of either Na+ or Mg2+, starting from in vivo ionic concentration to higher concentrations. Initially, an increase in ion concentration facilitates the structural distortion of individual ssDNA and helps to bring them close, and for this, Mg2+ is better than Na+. However, further addition of ions leads to structural reswelling of the DNA strands and inhibits their proximity. The structural changes are found to be guided by the strong interaction of the cations with the phosphinyl oxygen (pn_O). Additionally, a significant difference has been noticed in the interaction of the cations with phosphoester oxygen (pe_O) depending on the nature of the ion. The sequential and nonsequential base-pair stacking is one of the major factors in the structural collapse of individual ssDNA. Overall, the present investigation highlights some of the important aspects of aggregation of two ssDNA with the same base sequence at varying cationic concentration.

Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

“…3) suggest that both ssDNA and dsDNA undergo similar interactions with the counterions and coions in the BGE. The unexpected mobility plateaus observed at high ionic strengths (I R 0.6 M) suggest that counterion-counterion correlation effects (9,39,55-57), counterion-phosphate interactions (16), and/or cation-anion interactions in the BGE may contribute to the mobility plateaus observed for ssDNA and dsDNA at high ionic strengths.…”

“…2 with the solid curve describing the observed mobilities. The discrepancy can probably be attributed to an increase in flexibility and/or a decrease in the overall extension of the ssDNA molecules with increasing ionic strength because the persistence length decreases in a similar manner with increasing ionic strength (10)(11)(12)(13)(14)(15)(16)50).…”

“…The persistence length has been found to vary from 1.5 to 6 nm in solutions containing monovalent cations, depending on the size and sequence of the DNA (10,11) and the ionic strength of the solution (10)(11)(12)(13)(14)(15)(16). Some short ssDNA strands exhibit sequencedependent thermal transitions, suggesting that these oligomers have nonrandom conformations in solution (16)(17)(18)(19)(20)(21). Other ssDNA strands of the same size do not exhibit sequence-dependent thermal transitions, suggesting that their conformational ensembles primarily consist of unstructured molecules (20).…”

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

“…Free energy profile built using this method has been found to differentiate between structurally different assemblies of two DNAs in a previous work. [90] It is evident from Figure 11b that in presence of urea, it undergoes a huge structural change starting from the fully folded ensemble to a coil-like structure. As the structural parameters are concerned, conformations of protein are sampled over a wide range in the RMSD-R g space.…”

Effect of Stapling on the Thermodynamics of mdm2-p53 Binding

“…Although several other collective variables can be used to form this kind of conformational energy surface [54][55][56] RMSD and R g has been found useful in understanding the conformational transition in many cases. [57][58][59] The major energy minimum points in the energy landscape have been labeled with the uppercase alphabet and the conformation of the corresponding 9 . CC-BY 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”