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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

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

In polymer physics the 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 persistence length of molecule is much greater 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/s02 (s0 – sedimentation coefficient) or MD2 (D – translational diffusion coefficient) versus M (in the absence of volume effects) or n (number of monomers). In these coordinates the appearance of plateau will correspond to the complete impermeability of molecule and from plateau height the persistence length can be calculated.

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We analyzed literature data for a few synthetic polymers by our approach and determined their persistence lengths which values were very close to those in literature. Usually the synthesis of polymer molecules with very high molecular mass is 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 next stages: (1) a rigid rod-like particle, (2) a semi-rigid permeable coil and (3) an impermeable Gaussian coil (Serdyuk et al., 2007). We analyzed by our approach sedimentation data of DNA molecules from literature. It was shown that plateau starts from 40 000 base pairs of DNA molecule and the estimated value of persistence length was about 50 nm. This value is close to that from literature data (Lu et al., 2002). Thus, the proposed approach can be applied for flexibility analysis of biological macromolecules of different nature – from nucleic acids to proteins in strong denaturants.

References

    I.N. Serdyuk, N. Zaccai, and J. Zaccai (2007) Methods in molecular biophysics: Structure, function, dynamics. Cambridge University Press.

    Y. Lu, B. Weers, N.C. Stellwagen (2002). DNA persistence length revisited. Biopolymers 61, 261–275.


Anton V. Sergeev1
Natalia V. Lekontseva 2
Alexander A. Timchenko 2
Igor N. Serdyuk2

1Institute of Mathematical Problems of Biology Russian Academy of Sciences
Institutskaja str., 4
142290, Pushchino
Moscow Region, Russia
2Institute of Protein Research Russian Academy of Sciences
Institutskaja str., 4
142290, Pushchino
Moscow Region, Russia

Ph: +7 (4967) 318-504
Fx: +7 (4967) 318-500
antonsergeevphd@gmail.com