TY - CHAP
T1 - Exploring Cation Mediated DNA Interactions Using Computer Simulations
AU - He, Weiwei
AU - Kirmizialtin, Serdal
N1 - Funding Information:
We thank NYUAD for their generous support for the research. This research was carried out on the High-Performance Computing resources at New York University Abu Dhabi and the AD181 faculty research grant to S.K. Dr. Nawavi Naleem for careful reading of the work and Dr. Amit Srivastava for discussions.
Publisher Copyright:
© 2020, Springer Nature Switzerland AG.
PY - 2020
Y1 - 2020
N2 - Ion mediated interactions between nucleic acid helices are essential for their efficient packaging within tight spaces such as viral capsids, and nucleosomes. Understanding the fundamental rules governing these interactions is the key to design engineering tools in different length scales to achieve supramolecular architectures, leading to novel therapeutics, biosensors, and catalysis. As one of the building blocks for biology and biotechnology, DNA deserves special attention. However, the underlying physical principles governing DNA interactions with itself and its environment are still lacking. In this study, the mechanism of DNA attraction in the presence of divalent ions is investigated. The counter ion distributions and the conformational ensemble of parallel DNA strands are explored by conventional molecular dynamics and metadynamics simulations. Metadynamics simulation allows computing the free energy surface, providing a thermodynamic view to the DNA-DNA interaction. Our analysis reveals a strong correlation between the structure of the counterion atmosphere and inter-DNA interactions. The interaction energy is found to be mediated by the ions that bridge between the two DNA strands. In summary, computer simulations offer unprecedented detail into the dynamics and thermodynamics of DNA interactions that can potentially help to understand the biological DNA and also develop novel DNA based nanotechnologies.
AB - Ion mediated interactions between nucleic acid helices are essential for their efficient packaging within tight spaces such as viral capsids, and nucleosomes. Understanding the fundamental rules governing these interactions is the key to design engineering tools in different length scales to achieve supramolecular architectures, leading to novel therapeutics, biosensors, and catalysis. As one of the building blocks for biology and biotechnology, DNA deserves special attention. However, the underlying physical principles governing DNA interactions with itself and its environment are still lacking. In this study, the mechanism of DNA attraction in the presence of divalent ions is investigated. The counter ion distributions and the conformational ensemble of parallel DNA strands are explored by conventional molecular dynamics and metadynamics simulations. Metadynamics simulation allows computing the free energy surface, providing a thermodynamic view to the DNA-DNA interaction. Our analysis reveals a strong correlation between the structure of the counterion atmosphere and inter-DNA interactions. The interaction energy is found to be mediated by the ions that bridge between the two DNA strands. In summary, computer simulations offer unprecedented detail into the dynamics and thermodynamics of DNA interactions that can potentially help to understand the biological DNA and also develop novel DNA based nanotechnologies.
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U2 - 10.1007/978-3-030-47705-9_6
DO - 10.1007/978-3-030-47705-9_6
M3 - Chapter
AN - SCOPUS:85086117508
T3 - Lecture Notes in Bioengineering
SP - 51
EP - 63
BT - Lecture Notes in Bioengineering
PB - Springer
ER -