Oral Presentation 3

日時： 2020 年 10 月 29 日 15:45-17:15
チャンネル： ３

口頭発表３『分子ロボティクス』
Molecular robotics
座長： 佐藤 佑介 （東北大学）
Yusuke Sato (Tohoku University)
O3-01"Automated exploration of CRN generating DNA structures"Nathanael Aubert-Kato(Ochanomizu University)
O3-02"Optimization of the multi-step DNA computing reaction using oxDNA MD
simulation"
Shuntaro Sato
(School of Life Science and Technology, Tokyo Institute of Technology)
O3-03"Analysis of wireframe DNA nanostructure based on coarse-grained moleculardynamics simulated on a web server with simple interface"
Ibuki Kawamata(Tohoku University, Ochanomizu University)
O3-04"Simulation of Self-replication System with Virtual Spring Model"
Taisei Mori
(Tohoku University)

O3-01
Automated exploration of CRN generating DNA structures
Nathanael Aubert-Kato​1​​ ​naubertkato@is.ocha.ac.jp​

Alexandre Baccouche​2​alexandre.baccouche@unitn.it

Leo Cazenille​1
cazenille.leo@ocha.ac.jp

12

Department of Information Sciences, Ochanomizu University, Tokyo, JapanCIBIO, University of Trento, Trento, Italy

Keywords​: DNA nanostructures, chemical reaction networks, reaction enumeration, quality diversity
In recent years, a multitude of tools and models have been proposed for the rational design of specific DNAstructures [1]. In particular, families of structures ranging from a tetrahedron to large structures (“buckyball”)
can be created by chemical reaction networks (CRNs) using only a few different strands [2].
However, predicting what particular set of strands leads to a CRN generating DNA structures exhibiting
specific properties (size distribution, stability, and so) is challenging as it is an ill-defined and highly
dimensional problem, making exhaustive or random search inadequate. Here, we tackle this problem throughan automatic exploration of the range of possible DNA structures across a number of user-defined features ofinterests.
We use the MAP-Elites algorithm [3] to explore sets of initial strands: for each tested set of strands, wegenerate a CRN comprised of DNA structures and reaction paths among them with PepperCorn, anenumerator for DNA strand displacement reactions developed by Badelt et al. [4]. Promising results arecomplemented with NUPACK [5] analyses to identify which structures would be more prevalent for eachtested CRN. Our framework can thus automatically provide suggestions for experimental validation.

Figure: Workflow for automated discovery. The CRNs generated by sets of initial strands are evaluatedautomatically. Promising results are then forwarded to Nupack, which is used to annotate those CRNs.
[1] Seeman, N., Sleiman, H. "DNA nanotechnology." Nat Rev Mater 3, 17068 (2018)[2] He, Y. et al. "Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra." Nature 452 (2008)[3] Mouret, JB, et al. "Illuminating search spaces by mapping elites." arXiv:1504.04909 (2015).
[4] Badelt, S, et al. "A domain-level DNA strand displacement reaction enumerator allowing arbitrary
non-pseudoknotted secondary structures." Royal Society Interface 17.167 (2020)[5] Zadeh, JN, et al. "NUPACK: Analysis and design of nucleic acid systems." JCC 32.1 (2011)

O3-02
Optimization of the multi-step DNA computing reaction
using oxDNA MD simulation
Shuntaro Sato 1

sato.s.bg@m.titech.ac.jp

Masayuki Yamamura2
my@c.titech.ac.jp

Ken Komiya2

komiya@c.titech.ac.jp
12

School of Life Science and Technology, Tokyo Institute of Technology, J2-51, 4259,
Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
School of Computing, Tokyo Institute of Technology, J2-51, 4259, Nagatsuta-cho, Midori-ku,Yokohama, 226-8503, Japan

Keywords: DNA computing, State machine, Molecular Dynamics
Displacement Whiplash PCR (DWPCR) is a unique DNA computing reaction that implements astate machine [1]. In the DWPCR, each single-molecule DNA acts as a state transition machine byrepeating hairpin structure formation, DNA polymerase extension, and hairpin structure
deformation driven by primer extension under an isothermal condition. Each state transition istriggered upon addition of a 15-base DNA, called an operation signal. When the operation signal
DNA binds to the loop region of the hairpin DNA, DNA polymerase extends the operation signal
DNA as a primer and tears off the double-stranded stem region. The DWPCR, that can execute
multi-step computation, is expected to be applied for medical diagnosis implemented within anaqueous solution. However, only up to two-step state transitions have been reported so far [2].
In this study, we investigated the efficiency of DWPCR for achieving state transition ofthree–step and more by using oxDNA simulation [3, 4]. oxDNA is a software tool for molecular
dynamics (MD) simulation based on a coarse-grained model. At first, we performed MD simulationof an elementary process of the DWPCR and confirmed the DNA hairpin formation. Next, under
the same condition, we performed MD simulation of the process in which an operation signal DNA
was added to the hairpin DNA. As a result, the operation signal DNA did not bind to the loop
region of the hairpin DNA. This result agrees with that in our biochemical experiment. In thepresentation, we discuss the solution to the above problem and report the results of optimization ofthe reaction.
[1] Rose, J. A., Komiya, K., Yaegashi, S., Hagiya, M., Displacement Whiplash PCR: Optimized
Architecture and Experimental Validation, Lecture Notes in Computer Science, 4287:393-403,
2006.
[2] Komiya, K., Yamamura, M., Rose, J. A., Experimental validation and optimization of signal
dependent operation in whiplash PCR, Natural Computing, 9: 207–218, 2010.
[3] Ouldridge, T. E., Louis, A. A., Doye, J. P. K., Structural, mechanical, and thermodynamic
properties of a coarse-grained DNA model, J. Chem. Phys., 134: 085101, 2011.
[4] Snodin, B. E. K., Randisi, F., Mosayebi, M., Šulc, P., Schreck, J. S., Romano, F., Ouldridge, T.
E., Tsukanov, R., Nir, E., Louis, A. A., Doye, J. P. K., Introducing improved structuralproperties and salt dependence into a coarse-grained model of DNA, J. Chem. Phys., 142:234901, 2015.

O3-03
Analysis of wireframe DNA nanostructure
based on coarse-grained molecular dynamics
simulated on a web server with simple interface
Ibuki Kawamata 1,2

Yudai Yamashita 1

Kotaro Watanabe 1

kawamata@molbot.mech.tohoku.ac.jp yamashita@molbot.mech.tohoku.ac.jp watanabek@molbot.mech.tohoku.ac.jp

Sho Aradachi 1
aradachi@molbot.mech.tohoku.ac.jp12

Satoshi Murata 1
murata@molbot.mech.tohoku.ac.jp

Department of Robotics, School of Engineering, Tohoku University, 6-6-01, AramakiAzaAoba,Aoba, Sendai, Miyagi, 980-0845, Japan
Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka,Bunkyo-ku, Tokyo 112-8610, JapanKeywords: Molecular Robotics, DNA origami, coarse-grained molecular dynamics, web server
DNA origami is one of the most successful methodologies using self-assembly to fabricate anobject with a dimension about 100 nm and a resolution with a few nanometer [1,2]. Among various
types of DNA nanostructures, wireframe structure is of interest thanks to its shape versatility,rigidity, simplicity, and the space-efficiency [3,4]. To utilize such DNA nanostructure forapplication, it is important to analyze the stability under thermal fluctuation, the cavity size ofwireframe, and the effect of other molecules such as cationic ions [5]. To theoretically analyze
those characteristics, varieties of simulation tools have been developed [6], some of which were
not user-friendly due to its difficulty to setup.
Here, we developed a web server with a simple interface that can run a simulation and summarize
the results of oxDNA [7], which is a software based on coarse-grained molecular dynamics. Fig.1
is a screenshot of typical examples on the web server that offers an easy-to-use experience. We
further designed a simple wireframe DNA nanostructure and analyzed the behavior of it using theweb server. In the presentation, we will show our new results of the simulation and discuss thepotential benefit of our development.

Figure 1. (From left to right) Interface of web server to launch an oxDNA simulation.
Graphs of the simulation results. Snapshot of the simulation of smily face. Snapshot of thesimulation of wireframe structure.
[1] Yuki Suzuki, Ibuki Kawamata, Kohei Mizuno, Satoshi Murata, Large Deformation of a DNA‐ Origami Nanoarm Induced by theCumulative Actuation of Tension-Adjustable Modules, Angewandte Chemie International Edition , 59, 6230-6234, 2020
[2] Matthew R. Jones, Nadrian C. Seeman, Chad A. Mirkin, Programmable materials and the nature of the DNA bond , Science, 20,1260901, 2015[3] Taiki Watanabe, Yusuke Sato, Hayato Otaka, Ib uki Kawamata, Satoshi Murata, Shin Ichiro M. Nomura , DNA origami "quick"refolding inside of a micron -sized compartment, Molecules, 25, 2020
[4] Stephanie S. Simmel, Philipp C. Nickels, Tim Liedl, Wireframe and Tensegrity DNA Nanostructures, Accounts of ChemicalResearch, 6, 1691-1699, 2014
[5] Anuttara Udomprasert, Thaned Kangsamaksin, DNA origami applications in cancer therapy, Cancer Science, 108, 1535-1543,
2017[6] Hosna Jabbari, Maral Aminpour, Carlo Montemagno, Computational Approaches to Nucleic Acid Origami, ACS Combinatorial
Science, 17, 535-547, 2015[7] Benedict E. K. Snodin, Flavio Romano, Lorenzo Rovigatti, Thomas E. Ouldridge, Ard A. Louis, Jonathan P. K. Doye, Direct
Simulation of the Self-Assembly of a Small DNA Origami, ACS Nano, 10, 1724-1737, 2016

O3-04
Simulation of Self-replication System with Virtual Spring Model
Taisei Mori1

Ibuki Kawamata1,2Satoshi Murata1

mori@molbot.mech.tohoku.ac.jp

kawamata@molbot.mech.tohoku.ac.jp

murata@molbot.mech.tohoku.ac.jp

1

Department of Robotics, School of Engineering, Tohoku University, 6-6-01, AramakiAzaAoba, Aoba, Sendai,Miyagi, 980-0845, Japan
2
Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku,
Tokyo 112-8610, Japan

Chemical reactions play an important role in self-replication of biological organisms. Its process is complicatedto some extent, so a simulation model gives a powerful tool to understand it. As a simple description of a chemical
reaction system with various molecules, we consider a spring-mass-damper system[1] in which many elementsinteract with each other. In the past paper[1], an algorithm was proposed where the elements self-assemble into
different shapes depending on parameters such as spring constant/natural length and state transition rule set basedon the number of neighbors connected to the elements.
Here, we introduce the “state” as a new attribute of the simulation to improve the model’s expressiveness, inorder to simulate the process of self-replication. As the simplest example of self-replication, we deal with a stringof few interconnected elements, each of which has a different “state”. We examine how physical constants like aspring constant or a state transition rule influence the rate of self-replication.

[1] Kenichi Fujibayashi, Satoshi Murata, Ken Sugawara, Masayuki Yamamura, Self-Organizing Formation
Algorithm for Active Elements, IEEE 2002, 416-421[2] Kohji Tomita, Haruhisa Kurokawa, Satoshi Murata, Graph automata: natural expression of self-reproduction,
Physica D 171 (2002), 197–210[3] Rebecca Zhuo, Feng Zhou, Xiaojin He, Ruojie Sha, Nadrian C. Seeman, Paul M. Chaikin, Litters of selfreplicating origami cross-tiles, PNAS 116(2019), 1952-1957