Dalir H., Nisisako T., Yanagida Y., Hatsuzawa T.
Tokyo Institute of Technology, JP
Keywords: base-stacking interactions, double-helical DNA structure, hydrogen bond force, mechanical properties, single-molecule manipulation
The DNA molecule is the primary genetic material of most organisms. It is a double-helical biopolymer in which two chains of complementary wind around a common axis to form a double-helical structure. This paper aims at a comprehensive understanding of the novel elastic mechanical properties of single- and double-stranded DNA (ss-DNA/ds-DNA) molecules through experimental single-molecule manipulation. A general Newtonian elastic model for both single- and double-stranded biopolymers is proposed, and an explicit force-extension formula is introduced to characterize their deformations. The effective elastic properties of the DNA backbone are numerically extracted from the ss-DNA experiments. The mechanical properties of long ds-DNA molecules is then studied based on this model, where the base-stacking interactions originated from the weak van der Waals attractions between the polar groups of DNA adjacent nucleotide base pairs and the hydrogen bond force, which is the interaction between complementary bases are taken into account. Quantitative results are obtained by using the explicit force-extension formula and well agreement between theory and the single molecular experimental results were achieved. Via the simulation of stretching ds-DNA, some of the mechanical responses which can not be experimentally identified, including the twisting of the backbone, variation of the elastic deformation energy, base-stacking energy and hydrogen bond energy can be predicted.
Journal: TechConnect Briefs
Volume: 3, Nanotechnology 2008: Microsystems, Photonics, Sensors, Fluidics, Modeling, and Simulation – Technical Proceedings of the 2008 NSTI Nanotechnology Conference and Trade Show, Volume 3
Published: June 1, 2008
Pages: 685 - 688
Industry sector: Advanced Materials & Manufacturing
Topic: Informatics, Modeling & Simulation
ISBN: 978-1-4200-8505-1