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  RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations

Cruz-León, S., & Schwierz, N. (2022). RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations. The Journal of Physical Chemistry B. doi:10.1021/acs.jpcb.2c04488.

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Cruz-León, Sergio1, Author                 
Schwierz, Nadine1, 2, Author                 
Affiliations:
1Emmy Noether Research Group, Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2364691              
2Institute of Physics, University of Augsburg, Augsburg, Germany, ou_persistent22              

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 Abstract: The distribution of cations around nucleic acids is essential for a broad variety of processes ranging from DNA condensation and RNA folding to the detection of biomolecules in biosensors. Predicting the exact distribution of ions remains challenging since the distribution and, hence, a broad variety of nucleic acid properties depend on the salt concentration, the valency of the ions, and the ion type. Despite the importance, a general theory to quantify ion-specific effects for highly charged biomolecules is still lacking. Moreover, recent experiments reveal that despite their similar building blocks, DNA and RNA duplexes can react differently to the same ionic conditions. The aim of our current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 μs of simulation time. For the mono- and divalent cations Li+, Na+, K+, Cs+, Ca2+, Sr2+, and Ba2+, the simulations allow us to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes. The microscopic insights from the simulations display the origin of ion-specificity and shed light on the question of why DNA and RNA show opposing behavior in the same ionic conditions. Finally, the detailed binding patterns from the simulations reveal why RNA can capture more cations than DNA.

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Language(s): eng - English
 Dates: 2022-09-292022-06-282022-10-19
 Publication Status: Published online
 Pages: 9
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jpcb.2c04488
BibTex Citekey: cruz-leon_rna_2022
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Title: The Journal of Physical Chemistry B
  Abbreviation : J. Phys. Chem. B
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 1520-6106
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000293370_1