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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