80 A new approach in determining the rigidity of nucleic acids and polymers

• Published in: Journal of biomolecular structure & dynamics Vol. 31; no. sup1; pp. 51 - 52
• Main Authors: Sergeev, Anton V., Lekontseva, Natalia V., Timchenko, Alexander A., Serdyuk, Igor N.
• Format: Journal Article
• Language: English
• Published: Routledge 01.01.2013
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2013.786514

In polymer physics, persistence length of the chain molecules varying in degrees of stiffness is usually evaluated from hydrodynamic data for a set of polymers of different molecular mass М. It is known that from the extrapolation of translational diffusion coefficient to infinite molecular mass, one can calculate persistence length and hydrodynamic radius for rigid and semi-rigid molecules. If the persistence length of the molecule is much greater than its contour length, then the hydrodynamic parameters of the chain are independent of its size and such extrapolation is not applicable. In this case we proposed to plot the dependence M/s 0 2 (s 0 - sedimentation coefficient) or MD 2 (D - translational diffusion coefficient) vs. M (in the absence of volume effects) or n (number of monomers). In these coordinates the appearance of a plateau will correspond to the complete impermeability of the molecule and from plateau height the persistence length can be calculated. We analyzed literature data for a few synthetic polymers by our approach and determined their persistence lengths, the values of which were very close to those in the literature. Usually, the synthesis of polymer molecules with very high molecular mass is a very difficult task. But at the same time, natural polymers with high molecular mass are common in biology. A typical example is a DNA molecule. With increasing contour length of DNA, its conformation passes the next stages: (1) a rigid rod-like particle, (2) a semi-rigid permeable coil, and (3) an impermeable Gaussian coil (Serdyuk, Zaccai, & Zaccai, 2007 ). We analyzed by our approach sedimentation data of DNA molecules from the literature. It was shown that the plateau starts from 40,000 base pairs of the DNA molecule and the estimated value of persistence length was about 50 nm. This value is close to that from literature data (Lu, Weers, & Stellwagen, 2002 ). Thus, the proposed approach can be applied for flexibility analysis of biological macromolecules of different natures - from nucleic acids to proteins in strong denaturants.