Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session II

43 – POS Board 15 New Mechanical Transition Observed in Highly Stretched DNA with Constrained Linking Number Janusz W. Strzelecki 1 , Lukasz Peplowski 1 , Robert Lenartowski 2 , Wieslaw Nowak 1 , Aleksander Balter 1 . 1 Nicolaus Copernicus University, Torun, Poland, 2 Nicolaus Copernicus University, Torun, Poland. We report discovery of a new mechanical transition in stretched and topologically constrained DNA. We used a well established technique of stretching single molecules with an untreated Atomic Force Microscope tip to extend DNA. We explored the DNA mechanics under previously untested high stretching force regime, up to 1.8 nN of possible limit of sugar- phosphate backbone. We observed that if double helix is prohibited from rotation, then a transition is displayed as a small plateau in force vs. distance plot both during stretching and relaxation, at stretching forces approaching 1 nN. This transition was absent when molecules with rotational freedom were stretched, showing thus that underlying mechanism was directly connected with molecule linking number conservation. Such DNA behavior proves, that contrary to previous beliefs DNA duplex is not fully melted after undergoing two transitions reported before. Our all-atom steered molecular dynamics simulations of constrained and stretched DNA double helix showed the molecule forced to collapse and adapt a form similar to underwound P- DNA, with bases protruding outside of backbones at extensions correspnding to new transition. Thus, our preliminary hypothesis is that the observed increase in length in the new plateau is a result of reducing the diameter of a double helix through extreme stretching when unwinding is not possible. These results broaden our understanding of interplay of nanomechanics and topology of DNA. Additionally, recent research suggests that DNA could experience similar extreme conditions during abnormal mitosis. The behavior of highly deformed DNA is also important when considering this molecule as a potential bionanotechnology material. Strzelecki, J., Peplowski, L., Lenartowski, R., Nowak, W., & Balter, A. (2014). Mechanical transition in a highly stretched and torsionally constrained DNA. Physical Review E, 89(2), 020701.

44 – POS Board 16 RNA, Topology and Random Matrices Piotr Sulkowski 1,2 .

1 University of Warsaw, Faculty of Physics, Warszawa, Poland, 2 Caltech, Pasadena, CA, USA. To a given biopolymer, or a complex composed of several interconnected biopolymers, one can associate an auxiliary two-dimensional surface. A genus of this surface provides a very interesting topological characteristic of a given biopolymer (or a complex). I will discuss how random matrix theory can be used to classify all possible configurations of interacting biopolymers and determine their genus. Furthermore, I will present a new classification of known RNA structures based on their genus, and discuss the role of various types of base pairs in this classification.

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