Effect of Ionic Ordering in Conductivity Experiments of DNA Aqueous Solutions

Liubysh, O.O.; Alekseev, О. М.; Tkachov, S.Yu.; Perepelytsya, S. M.

doi:10.15407/ujpe59.05.0479

Cited by 10 publications

(12 citation statements)

References 31 publications

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“…6c ). The closed tweezers had a greater ionic conductivity compared with the buffer, consistent with molecular orbital theory and measurements of DNA systems with nanopores and dielectric spectroscopy 20 , 56 – 59 . The addition of dummy FUEL strands slightly decreased the overall ionic conductivity of the solution, suggesting a lower ionic conductivity for single strands in solution, as compared with tweezer structures.…”

Section: Resultssupporting

confidence: 79%

Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics

et al. 2019

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Detection of conformational changes in biomolecular assemblies provides critical information into biological and self-assembly processes. State-of-the-art in situ biomolecular conformation detection techniques rely on fluorescent labels or protein-specific binding agents to signal conformational changes. Here, we present an on-chip, label-free technique to detect conformational changes in a DNA nanomechanical tweezer structure with microwave microfluidics. We measure the electromagnetic properties of suspended DNA tweezer solutions from 50 kHz to 110 GHz and directly detect two distinct conformations of the structures. We develop a physical model to describe the electrical properties of the tweezers, and correlate model parameters to conformational changes. The strongest indicator for conformational changes in DNA tweezers are the ionic conductivity, while shifts in the magnitude of the cooperative water relaxation indicate the addition of fuel strands used to open the tweezer. Microwave microfluidic detection of conformational changes is a generalizable, non-destructive technique, making it attractive for high-throughput measurements.

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Section: Resultssupporting

confidence: 79%

Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics

et al. 2019

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“…Despite the difference of the potassium and sodium ions, such comparison makes sense because in atomistic molecular dynamics simulations in the present force field K + ions reveal the structure-making character of hydration and so do Na + ions in real solutions [61]. The calculated conductivity values are about 4 times lower than the experimental value for the DNA water solution without added salt obtained in the work [40]. However, we should note that the concentration of DNA in our simulations is about two orders of magnitude higher than in the experiments [37,40], while the ionic conductivity is known to decrease with the concentration of DNA [37].…”

Section: Discussionmentioning

confidence: 62%

“…The dynamics of the ions in water solutions may be characterized by the ionic current that appears under the action of the external electric filed. The experimental studies for DNA in water solution with the different salts of alkali metal ions show that the ionic conductivity essentially depends on the temperature, counterion type and concentration [35][36][37][38][39][40]. The de-pendence of conductivity on counterion type is featured by the ion size, charge and character of hydration [41].…”

Section: Introductionmentioning

confidence: 99%

“…The temperature dependence of the conductivity is related to the increase of the ion mobility with the temperature increase and with the conformational transformations of the DNA occurring due to the melting of the double helix [37,38]. The study of concentration dependence of ionic conductivity for DNA with KCl salt has shown that at salt concentrations lower than 0.4 M the conductivity of DNA solution is higher than the conductivity of KCl water solution without DNA [40]. This effect has been explained as the result of ordering of counterions around the DNA double helix in a lattice-like structure, the existence of which was studied by the specific ion-phosphate vibrations in the DNA low-frequency spectra <200 cm −1 [42,43].…”

Section: Introductionmentioning

confidence: 99%

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Dynamics of K$^+$ counterions around DNA double helix in the external electric field: a molecular dynamics study

Zdorevskyi¹,

Perepelytsya²

2020

Preprint

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The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K + counterions and for the system of KCl salt solution in the external electric field of different strength (up to 32 mV/ Å). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with KCl salt solution. The calculated values of ion mobility are within (0.05÷0.4) mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K + counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30 mV/ Å the double helix undergoes a phase transition from doublestranded to single-strand state.

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“…The existence of the lattice-like structure of DNA with counterions has been proved by the observation of the modes of ion-phosphate vibrations in the low-frequency Raman spectra of DNA (< 200 cm −1 ) [19][20][21][22][23][24]. The concept of ion-phosphate lattice has been proven to be useful for the description of different effects of DNA-counterion interaction [25,26].…”

Section: Introductionmentioning

confidence: 99%

Positively and negatively hydrated counterions in molecular dynamics simulations of DNA double helix

Perepelytsya¹

2019

Preprint

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The effects of positive and negative hydration of counterions (Na + , K + , and Cs + ) incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics approach. The results show that the dynamics of the hydration shell of counterions depends on region of ion localization around the macromolecule. The longest residence times have been observed for water molecules near the counterions that are localized in the minor groove of the double helix: about 30 ps in the case of Na + counterions and about 7 ps in the case of K + and Cs + counterions. In the major groove and outside the double helix it is essentially lower. The counterions constrain water molecules too strong, and as the result the effect of negative hydration for K + and Cs + counterions was not observed in the simulations. The analysis show that the effects of counterion hydration may be described better by using the water models with lower dipole moments.

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Effect of Ionic Ordering in Conductivity Experiments of DNA Aqueous Solutions

Cited by 10 publications

References 31 publications

Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics

Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics

Dynamics of K$^+$ counterions around DNA double helix in the external electric field: a molecular dynamics study

Positively and negatively hydrated counterions in molecular dynamics simulations of DNA double helix

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