Azimuthal Frustration and Bundling in Columnar DNA Aggregates

• Published in: Biophysical journal Vol. 84; no. 6; pp. 3607 - 3623
• Main Authors: Harreis, H.M., Likos, C.N., Löwen, H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-06-2003; Biophysical Society
• Subjects: Binding Sites; Biophysical Theory and Modeling; Computer Simulation; Deoxyribonucleic acid; DNA; DNA - chemistry; Electric Conductivity; Electrochemistry - methods; Energy Transfer; Macromolecular Substances; Models, Chemical; Models, Molecular; Molecular biology; Motion; Nucleic Acid Conformation; Phase Transition; Solutions - chemistry; Static Electricity
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/S0006-3495(03)75092-9

The interaction between two stiff parallel DNA molecules is discussed using linear Debye-Hückel screening theory with and without inclusion of the dielectric discontinuity at the DNA surface, taking into account the helical symmetry of DNA. The pair potential furthermore includes the amount and distribution of counterions adsorbed on the DNA surface. The interaction does not only depend on the interaxial separation of two DNA molecules, but also on their azimuthal orientation. The optimal mutual azimuthal angle is a function of the DNA-DNA interaxial separation, which leads to azimuthal frustrations in an aggregate. On the basis of the pair potential, the positional and orientational order in columnar B-DNA assemblies in solution is investigated. Phase diagrams are calculated using lattice sums supplemented with the entropic contributions of the counterions in solution. A variety of positionally and azimuthally ordered phases and bundling transitions is predicted, which strongly depend on the counterion adsorption patterns.