Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations

Yu, Binhan; Bien, Karina G.; Wang, Tianzhi; Iwahara, Junji

doi:10.1016/j.bpj.2022.06.022

Cited by 4 publications

(5 citation statements)

References 57 publications

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“…With only Na + , the net ion exchange with the bulk was not a significant factor, largely because any exchange of cations with the bulk would have to be accompanied by the concomitant exchange of anions (to maintain neutrality), but Cl – was not shown to be a major contributor to the mixing-entropy term in any case (Table ). For this reason, we expect that systems with only a single cation species or with mixtures of like-valence cations with similar charge density (e.g., Na + and K + ) would also have negligible mixing entropies associated with interhelical orientation. , However, it would be interesting to see whether entropic effects stemming from ion exchange also arise with mixtures of different valence coanions (e.g., Cl – and SO 4 2– ).…”

Section: Discussionmentioning

confidence: 99%

“…For this reason, we expect that systems with only a single cation species or with mixtures of like-valence cations with similar charge density (e.g., Na + and K + ) would also have negligible mixing entropies associated with interhelical orientation. 68,69 However, it would be interesting to see whether entropic effects stemming from ion exchange also arise with mixtures of different valence coanions (e.g., Cl − and SO 4…”

Section: ■ Conclusionmentioning

confidence: 99%

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Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations

Templeton,

Hamilton,

Russell

et al. 2023

J. Phys. Chem. B

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Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Forster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson−Boltzmann (PB) calculations for monovalent salt (Na + ). However, PB underestimated the ability of mixtures of monovalent and divalent ions (Mg 2+ ) to reduce the conformational preference. As a complementary approach, we performed all-atom molecular dynamics (MD) simulations and found better agreement with the experimental results. While MD and PB predict similar electrostatic forces, MD predicts a greater accumulation of Mg 2+ in the ion atmosphere surrounding the DNA. Mg 2+ occupancy is predicted to be greater in conformations close to the parallel orientation than in conformations close to the crossed orientation, enabling a greater release of Na + ions and providing an entropic gain (one bound ion for two released). MD predicts an entropy gain larger than that of PB because of the increased Mg 2+ occupancy. The entropy changes have a negligible effect at low Mg 2+ concentrations because the free energies are dominated by electrostatic repulsion. However, as the Mg 2+ concentration increases, charge screening is more effective and the mixing entropy produces readily detectable changes in packing preferences. Our results underline the importance of mixing entropy of counterions in nucleic acid interactions and provide a new understanding on the impact of a mixed ion atmosphere on the packing of DNA helices.

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Section: Discussionmentioning

confidence: 99%

Section: ■ Conclusionmentioning

confidence: 99%

Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations

Templeton,

Hamilton,

Russell

et al. 2023

J. Phys. Chem. B

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“…Many researchers have used different values for ionic radii in their comparisons and calculations. Some have used the fully dehydrated ionic radii, while others have used variations of coordinated ions with varying degrees of hydration. ,,,,,,, Many studies have suggested that ionic radii are necessary to consider when comparing nucleic acid stability or competitive ion binding in different solutions ,, while others suggest no such comparison is necessary. ,, In this work, the ionic radius for each of the alkali metals had a linear relationship with the destabilization of RNA duplexes (Figure S8) and was, therefore, used as a variable in the correction factor.…”

Section: Discussionmentioning

confidence: 99%

“…36,39−41 Many of those studies have shown conflicting results regarding the preferential occupancy of the ion atmosphere. 13,40,46,110,115,116 Regardless, these studies have provided benchmarks for electrostatic association calculations of metal ions around nucleic acids. The study presented here has shown measurable differences in ΔG°3 7 for nucleic acids that are dependent on the fraction of GC pairs in an RNA duplex, the identity of alkali metal ions in the solution, and the concentration at which those metal chlorides are mixed.…”

Section: T H Imentioning

confidence: 99%

“…15,36,39,40,98,110,113,114 Many studies have suggested that ionic radii are necessary to consider when comparing nucleic acid stability or competitive ion binding in different solutions 46,110,115 while others suggest no such comparison is necessary. 13,40,116 In this work, the ionic radius for each of the alkali metals had a linear relationship with the destabilization of RNA duplexes (Figure S8) and was, therefore, used as a variable in the correction factor.…”

Section: ■ Introductionmentioning

confidence: 99%

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Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability

Arteaga,

Dolenz,

Znosko

2023

ACS Omega

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The nonspecific atmosphere around nucleic acids, often termed the ion atmosphere, encompasses a collection of weak ion−nucleic acid interactions. Although nonspecific, the ion atmosphere has been shown to influence nucleic acid folding and structural stability. Studies investigating the composition of the ion atmosphere have shown competitive occupancy of the atmosphere between metal ions in the same solution. Many studies have investigated single ion effects on nucleic acid secondary structure stability; however, no comprehensive studies have investigated how the competitive occupancy of mixed ions in the ion atmosphere influences nucleic acid secondary structure stability. Here, six oligonucleotides were optically melted in buffers containing molar quantities, or mixtures, of either XCl (X = Li, K, Rb, or Cs) or NaCl. A correction factor was developed to better predict RNA duplex stability in solutions containing mixed XCl/NaCl. For solutions containing a 1:1 mixture of XCl/NaCl, one alkali metal chloride contributed more to duplex stability than the other. Overall, there was a 54% improvement in predictive capabilities with the correction factor compared with the standard 1.0 M NaCl nearest-neighbor models. This correction factor can be used in models to better predict RNA secondary structure in solutions containing mixed XCl/NaCl.

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The soft breeze of the cation atmosphere around DNA

Ferrage¹,

Laage²

2022

Biophysical Journal

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Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations

Cited by 4 publications

References 57 publications

Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations

Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations

Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability

The soft breeze of the cation atmosphere around DNA

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