ArticleNucleic acids research2003
A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 83 citations in OpenAlex.
- Effects of synergistic/antagonistic interactions between spermidine (3+) and putrescine (2+) on gene expression through higher-order DNA structural modification.European biophysics journal : EBJ · 2026Article
- Sequence-defined polymers for predictable gene delivery.Nature reviews. Chemistry · 2026Review
- Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.The journal of physical chemistry. B · 2023Article
- Specific effects of antitumor active norspermidine on the structure and function of DNA.Scientific reports · 2019Article
- Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4.Nucleic acids research · 2019Article
- Sequence-dependent DNA condensation as a driving force of DNA phase separation.Nucleic acids research · 2018Article
- Adaptive resolution simulations of biomolecular systems.European biophysics journal : EBJ · 2017Review
- Water Dynamics in the Hydration Shells of Biomolecules.Chemical reviews · 2017Review
- Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex.Biophysical journal · 2017Article
- Melting of polymeric DNA double helix at elevated temperature: a molecular dynamics approach.Journal of molecular modeling · 2017Article
- Molecular dynamics study on the mechanism of polynucleotide encapsulation by chitosan.Scientific reports · 2017Article
- Order and interactions in DNA arrays: Multiscale molecular dynamics simulation.Scientific reports · 2017Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
- Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs.Journal of computer-aided molecular design · 2014Article
- Ion counting from explicit-solvent simulations and 3D-RISM.Biophysical journal · 2014Article
- Why double-stranded RNA resists condensation.Nucleic acids research · 2014Article
- Intensities of DNA ion-phosphate modes in the low-frequency Raman spectra.The European physical journal. E, Soft matter · 2010Article
- Molecular dynamics simulations of DNA-polycation complex formation.Biophysical journal · 2009Article
- Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.The journal of physical chemistry. B · 2008Article
- Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method.Biochemistry · 2007Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Four different molecular dynamics (MD) simulations have been performed for ordered DNA decamers, d(5'-ATGCAGTCAG)*d(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine3+ (Spd3+) and putrescine2+ (Put2+), the synthetic polyamine diaminopropane2+ (DAP2+) and Na+. The simulation set-up corresponds to an infinite array of parallel DNA mimicking the state in oriented DNA fibers or crystals. This work describes general properties of polyamine and Na+ binding to DNA. Simulated diffusion coefficients show satisfactory agreement with experimental NMR diffusion data of comparable systems. The interaction of the polyamines with DNA is dynamic in character and the cations mostly form short-lived contacts with the electronegative binding sites of DNA. Polyamines, Na+ and water interact most frequently with the charged phosphate atoms with preference for association from the minor groove side with O1P over O2P. There is a strong anti-correlation in the cation binding to the electronegative groups of DNA, i.e. the presence of a cation near one of the DNA sites repels other cations from binding to this and to the other sites separated by <7.5 A from each other. In contrast to the other polyamines, DAP2+ is able to form 'bridges' connecting neighboring phosphate groups along the DNA strand. A small fraction of DAP2+ and Put2+ can be found in the major grooves, while Spd3+ is absent there. The results of the MD simulations reveal principal differences in the polyamine-DNA interactions between the natural (Spd3+, Put2+ and spermine4+) and synthetic (DAP2+) polyamines.
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