Torsional deformation of double helix in interaction and aggregation of DNA

Journal of Physical Chemistry B

Volumn 108, Issue 20, 2004, Pages 6508-6518

  Cherstvy, A G ^a,d   Kornyshev, A A ^b   Leikin, S ^c  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^d B I STEPANOV INSTITUTE OF PHYSICS   (Belarus)

Author keywords

[No Author keywords available]

Indexed keywords

AGGLOMERATION; CELLS; DEFORMATION; DNA SEQUENCES; ELASTICITY; ELECTROSTATICS; FREE ENERGY; MOLECULAR ORIENTATION; MOLECULAR STRUCTURE; VIRUSES;

DNA-DNA INTERACTION; DOUBLE HELIX STRUCTURES; TORSIONAL DEFORMATION; TORSIONAL ELASTICITY;

DNA;

EID: 2642527925     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0380475     Document Type: Article

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53. c) ∼ 1.
54. Here we account for charge "smearing" caused by finite width and thermal motions of charged groups (in contrast to the approximation of infinitely thin charged lines for strands and grooves used in our previous studies). For simplicity, we assume that the smearing can be described by a Gaussian function with the width w independent of charge group identity and location. Such smearing suppresses the contribution of the interaction mode with n = 2, as compared to the case of w = 0.
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57. In principle, an even more accurate approximation would be based on using an independent variational parameter as a factor in front of the second integral. However, the resulting expanded set of trial functions gives exactly the same result for infinitely long helices and only minor corrections for finite-length helical fragments.
58. i(z)).
59. 0 (cf. Figure 3a,b and Figure 5b). This frustration of pairwise alignment is caused by multimolecular correlations. It leads to a rather shallow energy minimum at the optimal alignment, and therefore, it might result in substantial thermal torsional fluctuations. Such fluctuations reduce biaxial correlations and might cause complete loss of the long-range order in azimuthal orientations. Although this effect might be important for understanding the loss of cholesteric packing of molecules at small interaxial distances, its detailed analysis is beyond the scope of the present work.