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Volumn 129, Issue 48, 2007, Pages 14981-14988

Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC EMISSION SPECTROSCOPY; CHEMICAL ANALYSIS; CHROMOSOMES; DECOMPOSITION; IONS; THERMODYNAMICS;

EID: 36848999901     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja075020g     Document Type: Article
Times cited : (224)

References (53)
  • 3
    • 1242274330 scopus 로고    scopus 로고
    • Draper, D. E. RNA 2004, 10, 335-343.
    • (2004) RNA , vol.10 , pp. 335-343
    • Draper, D.E.1
  • 21
    • 36849032397 scopus 로고    scopus 로고
    • For salt-dependent folding or ligand-binding reactions, ion-binding isotherms have typically been fit to a polynomial binding model based on the simple mass action equilibrium. However, this equilibrium is not a physical description of the long-range electrostatic interactions governing the behavior of the ion atmosphere. Further, the exclusion of anions is typically neglected in these analyses, a condition that is only satisfied for very low salt concentration (0.01 M, refs 9, 20).
    • For salt-dependent folding or ligand-binding reactions, ion-binding isotherms have typically been fit to a polynomial binding model based on the simple mass action equilibrium. However, this equilibrium is not a physical description of the long-range electrostatic interactions governing the behavior of the ion atmosphere. Further, the exclusion of anions is typically neglected in these analyses, a condition that is only satisfied for very low salt concentration (0.01 M, refs 9, 20).
  • 23
    • 36849004587 scopus 로고    scopus 로고
    • + ions in the atmosphere may be close enough to experience relaxation from the DNA but others may not be. Further, the ion distribution can change with ionic conditions. Quantitatively comparing results over a series of conditions is difficult.
    • + ions in the atmosphere may be close enough to experience relaxation from the DNA but others may not be. Further, the ion distribution can change with ionic conditions. Quantitatively comparing results over a series of conditions is difficult.
  • 28
    • 36849078974 scopus 로고    scopus 로고
    • Dye association has complex thermodynamics as neutral dye-indicators may bind to metal ions that are free or part of the ion atmosphere, although presumably there is partial or extensive exclusion of the dye-bound metal ion from the atmosphere because of the preference for smaller cations in the atmosphere
    • Dye association has complex thermodynamics as neutral dye-indicators may bind to metal ions that are free or part of the ion atmosphere, although presumably there is partial or extensive exclusion of the dye-bound metal ion from the atmosphere because of the preference for smaller cations in the atmosphere.
  • 30
    • 0037928815 scopus 로고    scopus 로고
    • Das, R.; Mills, T. T.; Kwok, L. W.; Maskel, G. S.; Milien, I. S.; Doniach, S.; Finkelstein, K. D.; Herschlag, D.; Pollack, L. Phys. Rev. Lett. 2003, 90, 188103:1-4.
    • Das, R.; Mills, T. T.; Kwok, L. W.; Maskel, G. S.; Milien, I. S.; Doniach, S.; Finkelstein, K. D.; Herschlag, D.; Pollack, L. Phys. Rev. Lett. 2003, 90, 188103:1-4.
  • 32
    • 0345983583 scopus 로고    scopus 로고
    • Leontes, N. B, SantaLucia, J, Jr, Eds, American Chemical Society: Washington, DC
    • Macke, T.; Case, D. A. Molecular Modeling of Nucleic Acids; Leontes, N. B., SantaLucia, J., Jr., Eds.; American Chemical Society: Washington, DC, 1998; pp 379-393.
    • (1998) Molecular Modeling of Nucleic Acids , pp. 379-393
    • Macke, T.1    Case, D.A.2
  • 34
  • 36
    • 36849048400 scopus 로고    scopus 로고
    • As discussed in the Introduction, the Manning theory, although often quoted, is a highly simplified treatment of the ion atmosphere. Manning theory partitions the ion atmosphere into condensed ions, directly attached to the macromolecule, and mobile ions, whose interactions are treated in a linearized Poisson-Boltzmann model. Our method measures all of the thermodynamically associated ions, which includes the condensed ions and contributions from the mobile ions in the Manning framework. Manning theory predicts the total number of excluded anions to be 0.06 ions per charge, independent of salt concentration. Experimentally, we find that the balance between associated counterions and excluded anions does change as a function of total salt concentration (Figure 3, in disagreement with the Manning prediction. Furthermore, we find that even at the lowest concentration studied 5 mM Na, the number of excluded anions is
    • +) the number of excluded anions is 0.11 ± 0.03 per charge. This indicates that even at these low ion concentrations Manning theory is, at best, approximate.
  • 43
    • 0036009329 scopus 로고    scopus 로고
    • Egli, M. Chem. Biol. 2002, 9, 277-286.
    • (2002) Chem. Biol , vol.9 , pp. 277-286
    • Egli, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.