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Volumn 70, Issue 5, 2004, Pages 12-

DNA-DNA interaction beyond the ground state

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; COMPUTER SIMULATION; ELECTROSTATICS; GENES; GROUND STATE; HEURISTIC METHODS; LIQUID CRYSTALS; MONTE CARLO METHODS;

EID: 41349095197     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.70.051913     Document Type: Article
Times cited : (24)

References (48)
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    • This approach has been used in the past to solve other problems involving path integrals for 1D systems D. J. Scalapino, M. Sears, and R. A. Ferrell, Phys. Rev. BPLRBAQ0556-280510.1103/PhysRevB.6.3409 6, 3409 (1972);
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  • 34
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    • Or to put it another way, the ground state wave function should be periodic in (Formula presented), since our starting potential was periodic
    • Or to put it another way, the ground state wave function should be periodic in (Formula presented), since our starting potential was periodic.
  • 35
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    • I. V. Yurkevich and I. V. Lerner, Phys. Rev. BPRBMDO0163-182910.1103/PhysRevB.63.064522 63, 064522 (2001), and references contained therein.
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    • Yurkevich, I.V.1    Lerner, I.V.2
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    • 0001739743 scopus 로고    scopus 로고
    • I. F. Herbut, Phys. Rev. BPRBMDO0163-182910.1103/PhysRevB.61.14723 61, 14723 (2000), and references contained therein.
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    • addition, the “QM” analysis has clarified the generic features of excitation of soliton modes and their contribution to the interaction
    • In addition, the “QM” analysis has clarified the generic features of excitation of soliton modes and their contribution to the interaction.
  • 39
    • 0001301693 scopus 로고    scopus 로고
    • A theory of Shklovskii [B. I. Shklovskii, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.60.5802 60, 5802 (1999);
    • (1999) Phys. Rev. E , vol.60 , pp. 5802
    • Shklovskii, B.I.1
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    • T. T. Nguyen, I. Rouzina, and B. I. Shklovskii, J. Chem. Phys.JCPSA60021-960610.1063/1.480819 112, 2562 (2000)] has claimed that triply charged counterions of the buffer electrolyte are capable of building nonlinear patterns: “Wigner crystals.” Such patterns can provide charge separation motifs around negatively charged macromolecules, even if the latter were homogeneously charged rods. When formed, these nonlinear structures can cause attraction between the parallel rods, as positively charged sections around one rod can set in front of bare, negatively charged sections of another rod. These findings had a resonance in relation with a more general phenomenon, the so-called “anomalous” attraction between similarly charged colloid particles
    • (2000) J. Chem. Phys. , vol.112 , pp. 2562
    • Nguyen, T.T.1    Rouzina, I.2    Shklovskii, B.I.3
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    • A. K. Arora and B. V. R. Tata
    • Ordering and Phase Transitions in Charged Colloids, edited by A. K. Arora and B. V. R. Tata (VCH, New York, 1996)]. The stratified counterion clouds surrounding the charged rods are not pinned and are free to slide along the rod axis. The assemblies built of such molecules will be therefore lacking any azimuthal correlations. However, it is well known that such correlations exist, otherwise, it would not have been possible to observe the helical structure of DNA in columnar phases, as it has been done in classical experiments
    • (1996) Ordering and Phase Transitions in Charged Colloids
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    • S. B. Zimmermann and B. H. Pfeiffer, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 76, 2703 (1979)]. In reality, the helical structure of the charge distribution of phosphates of the DNAs may cause pinning, and the two effects—Wigner crystal formation and DNA helical structure—may produce DNA-structure-sensitive nonlinear patterns. The study of such phenomena is a challenging task for theory and simulations. However, we believe that (i) the helical structure of DNA is always there, and this alone will cause charge separation motif for the chemisorbed counterions; (ii) the attraction exists not only for triply charged ions but for singly and doubly charged ions ((Formula presented), (Formula presented) are good DNA condensers), here Wigner crystals are unlikely; (iii) the polyanions such as spermine, spermidine, and protamine cannot be considered as point charges but rather a system of connected single charges envisaged as adsorbing in a wormlike fashion into the DNA grooves. Thus experimental data can be explained by a simpler model, not involving Wigner crystal formation.10.1073/pnas.76.6.2703
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  • 46
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    • The counterion distributions might not necessarily be rigid. A model of the temperature-assisted rearrangements of counterions between the minor and major grooves has been suggested [A. Cherstvy, A. A. Kornyshev, and S. Leikin, J. Phys. Chem. BJPCBFK1089-564710.1021/jp026343w 106, 13362 (2002)] offering an explanation of the temperature induced DNA condensation observed in solution of manganese salts
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    • Cherstvy, A.1    Kornyshev, A.A.2    Leikin, S.3
  • 47


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.