Ionic liquids make DNA rigid

Abstract

Persistence length of double-stranded DNA (dsDNA) is known to decrease with an increase in ionic concentration of the solution. In contrast to this, here we show that the persistence length of dsDNA increases dramatically as a function of ionic liquid (IL) concentration. Using all atom explicit solvent molecular dynamics simulations and theoretical models, we present, for the first time, a systematic study to determine the mechanical properties of dsDNA in various hydrated ILs at different concentrations. We find that dsDNA in 50 wt % ILs have lower persistence length and stretch modulus in comparison to 80 wt % ILs. We further observe that both the persistence length and stretch modulus of dsDNA increase as we increase the concentration of ILs. The present trend of the stretch modulus and persistence length of dsDNA with IL concentration supports the predictions of the macroscopic elastic theory, in contrast to the behavior exhibited by dsDNA in monovalent salt. Our study further suggests the preferable ILs that can be used for maintaining DNA stability during long-term storage.

Short DNA persistence length in a mesoscopic helical model

“…The orientational correlation between distant portions of the helical molecule may be lost due to disordering thermal fluctuations or to interactions with the surrounding solvent. Such effects vary both with the sequence specificities and type of solvent [28] thus concurring to determine the flexibility properties as measured by the l p [29]. For semi-flexible polymers the latter is defined as the characteristic decay length of the correlation between two bond vectors, d i ≡ d i,i−1 and d k ≡ d k,k−1 , that is:…”

Pressure-Dependent Stability of Imidazolium-Based Ionic Liquid/DNA Materials Investigated by High-Pressure Infrared Spectroscopy

“…The alkyl side chain of an imidazolium cation may participate in aggregation and association with anions in bulk ILs, although the hydrophilic and Coulomb forces remain the dominant interactions [11][12][13][14][15]. On top of that, several reports [17][18][19][20][21][22][23][24] show that the hydrophobic alkyl chains can stabilize biopolymers like nucleic acids via forming the association through electrostatic interactions between the DNA molecule and cations of IL.DNA molecules can associate with cations of IL via the negatively charged backbone and hydrophobic groove interaction of DNA [19][20][21][22][23][24]. The cluster structure of ILs can be disturbed by mixing with an additive-like DNA via electrostatic interaction between the cation head group of ILs and phosphate anion of DNA and hydrophobic association between the alkyl part of IL cation and the groove region or nitrogenous base of DNA [19][20][21][22][23][24].…”

“…Part of base pairs (pyrimidine and purine), which interact via hydrogen bonding and stacking, are easily attracted to alkyl tail of ILs with noncovalent interaction, hydrophobic interaction, or van der Waals force. Several researchers [19][20][21][22] have suggested that the chemical structure of the cationic head group of ILs determines the electrostatic interaction to a certain extent, whereas the alkyl chain length of the cation is responsible for the stability of groove association. Ghoshdastidar et al [25] have reported that ILs can rescue DNA by forming a complex via specific trapping force in water solutions.…”

“…The conformation of DNA-IL complexes in an aqueous solution or in neat ILs reveals that the durability depends on the hydration and cation binding, which can be adjusted by varying ILs and constituent concentrations. The ILs that can spontaneously self-assemble and specifically attach to groove and backbone structures allow to skillfully control the DNA structure [19,20,25].High pressure allows to force ions or molecules into close-range to enhance the interactions between them, which makes it a useful and effective technique. Previous studies [26][27][28] revealed that pure ILs have an anisotropic cluster structure, and the hydrogen-bonding network can be easily disturbed by adding various materials under high-pressure conditions.…”

“…The alkyl side chain of an imidazolium cation may participate in aggregation and association with anions in bulk ILs, although the hydrophilic and Coulomb forces remain the dominant interactions [11][12][13][14][15]. On top of that, several reports [17][18][19][20][21][22][23][24] show that the hydrophobic alkyl chains can stabilize biopolymers like nucleic acids via forming the association through electrostatic interactions between the DNA molecule and cations of IL.…”