Solvent effects on the conformation of DNA dodecamer segment: A simulation study

Shen, Xin; Gu, Bing-Lin; A.A., Sushkov; Zhang, F. S.

doi:10.1063/1.3610549

Cited by 26 publications

(30 citation statements)

References 76 publications

(84 reference statements)

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“…72,82 Furthermore, the size of dehydrated Cs + is too large to fit the cavity of the G-quartet. 87 Further addition of salts leads to a decrease in R h , which is the result of the formation of the G-quadruplex and the decrease in the intramolecular electrostatic repulsion as discussed before, and the concentration required to induce a decrease in R h of each cation obeys the order K + (B10.0 mM) o Na + (B100.0 mM) o Cs + E Li + (B1.0 mM). 7(a).…”

Section: View Article Onlinementioning

confidence: 76%

The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation

Gao

2016

Soft Matter

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A human telomere DNA segment (HT-DNA) can fold into a G-quadruplex in the presence of some monovalent cations. These cations can interact with the phosphate groups of the DNA segment and/or with the O6 oxygen atom of guanines, which are called non-specific interactions and specific interactions, respectively. However, until now how these two interactions affect the structure of HT-DNA has not been well understood. In this study, a combination of analytical ultracentrifugation (AUC) and circular dichroism (CD) was used to explore the effects of these two interactions on the structure of a 22-mer single-stranded DNA with a sequence of 5'-AGGG(TTAGGG)3-3'. The results showed that the standard sedimentation coefficient (s20,w) of HT-DNA starts to increase when the concentration of potassium ions (CK(+)) is higher than 10.0 µM due to the formation of a G-quadruplex through specific interactions. Whereas, for a control DNA, a higher CK(+) value of 1.0 mM was needed for increasing s20,w due to non-specific interactions. Moreover, potassium ions could promote the formation of the G-quadruplex much more easily than lithium, sodium and cesium ions, presumably due to its appropriate size in the dehydrated state and easier dehydration. The molar mass of DNA at different cation concentrations was nearly a constant and close to the theoretical value of the molar mass of monomeric HT-DNA, indicating that what we observed is the structural change of individual DNA chains.

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Section: View Article Onlinementioning

confidence: 76%

The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation

Gao

2016

Soft Matter

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“…[69][70][71] The counter ion layer is too stable to be removed by conventional deionization methods. However recent research found that an electric field can promote the dissociation of the DNA-ion complex during capillary electrophoresis resulting in irregular DNA migration velocity.…”

Section: Dnmp Phosphate Association With Sodium Ionsmentioning

confidence: 99%

Electrophoretic Transport of Single DNA Nucleotides through Nanoslits: A Molecular Dynamics Simulation Study

et al. 2015

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There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with two or more detectors. We performed molecular dynamics simulations of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits with both smooth and rough walls. The electric field (E) varied from 0.0 to 0.6 V/nm. The nucleotides adsorb and desorb from walls multiple times during their transit through the slit. The nucleotide-wall interactions differed due to nucleotide hydrophobicities and wall roughness which determined duration and frequency of nucleotide adsorptions and their velocities while adsorbed. Transient association of nucleotides with one, two, or three sodium ions occurred, but the mean association numbers (ANs) were weak functions of nucleotide type. Nucleotide-wall interactions contributed more to separation of nucleotide flight time distributions than ion association and thus indicate that nucleotide-wall interactions play a defining role in successfully discriminating between nucleotides on the basis of their flight times through nanochannels/slits. With smooth walls, smaller nucleotides moved faster, but with rough walls larger nucleotides moved faster due to fewer favorable wall adsorption sites. This indicates that roughness, or surface patterning, might be exploited to achieve better time-of-flight based discrimination between nucleotides.

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“…After that, the following simulations of 60 ns are carried out for dynamics and structure analyses. The structure parameters are analyzed by the program Curves [46][47][48][49] continually for the precise values (the width and depth of the minor groove are defined in detail in Ref. [46]).…”

Section: Theory and Simulation Detailsmentioning

confidence: 99%

Competition between Na+and Rb+in the minor groove of DNA

2012

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The competition between Na⁺ and Rb⁺ ions in the minor groove of a synthetic B-DNA dodecamer d (CGCGAATTCGCG) is studied using molecular dynamics simulations as the ratio of these two ions changing from 9:1 to 1:9 with the DNA merged into the solvent of water molecule at 298 K. When the concentration of Rb⁺ ions increases, from minority to majority, Na⁺ ions are gradually released from the A tract, and the binding sites in the minor groove are occupied by Rb⁺ ions, extending from the A tract to the whole minor groove. Comparing Na⁺ with Rb⁺ ions, the conformation of the minor groove is influenced strongly by Na⁺ ions.

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Solvent effects on the conformation of DNA dodecamer segment: A simulation study

Cited by 26 publications

References 76 publications

The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation

The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation

Electrophoretic Transport of Single DNA Nucleotides through Nanoslits: A Molecular Dynamics Simulation Study

Competition between Na+and Rb+in the minor groove of DNA

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