C-5-46
Acceleration of DNA strand exchange reaction by cationic
comb-type copolymers
Naohiko Shimada 1

Wei Song 2

nshimada@bio.titech.ac.jp

songwei@ms.ifoc.kyushu-u.ac.jp

Atsushi Maruyama 1
amaruyama@bio.titech.ac.jp

1

School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology,
4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa Pref. 226-8501, Japan2
Departments in Graduate School of Engineering, Kyushu University,744, Motooka, Nishi-ku,Fukuoka, 819-0395, Japan

Keywords: molecular robotics, cationic polymers, DNA strand exchange reactionDNA strand exchange reaction (SER) between double-stranded DNA(dsDNA) and its
complementary single-stranded DNA(ssDNA) is a key reaction in biotechnological applications(1)There are many reports describing DNA nanomachines triggered by the SER. Highly programed
SER has been exploited to build DNA logic gate (2). In these application, the dsDNAs generally
have sticky end as known as toehold in order to control rate of the SER because of very slow rateof SER between dsDNA having blunt end and ssDNA. In nature, recombination proteins promote
the SER even in DNA having blunt end. However, the applications of the proteins to DNA
biotechnology based on the SER are limited by the instability and resource ineffectiveness of theproteins. An artificial agent showing the activity of the proteins has been desired for theapplication of the DNA biotechnology including molecular robotics.
We have previously demonstrated that cationic comb type copolymers consisting of polycation
backbone and abundant hydrophilic graft chain influence kinetics and thermodynamics of nucleic
acid hybrid under physiologically relevant condition. For example, poly( L -lysine)-graft-dextran(PLL-g-Dex) copolymer significantly accelerates DNA hybridization over 200-folds(3).
Moreover, the copolymer markedly accelerated the SER by 4-5 orders of magnitude (4), whilestabilizing dsDNA DNA (5). However, the stabilization of dsDNA is considered to be principally
unfavorable for acceleration of the SER, because partial dissociation of dsDNA is required for an
initial step of SER. In this study, we focused on urea which is a well-known destabilizing agent
for dsDNA, we prepared cationic comb type copolymers partially modified with urea (ureido)groups, poly(allylamine-co-allylurea)-graft-dextran. The copolymers showed higher acceleration
effect of SER than unmodified copolymer.
[1]Zhang, D.Y. and Seelig, G. (2011) Dynamic DNA nanotechnology using strand-displacement
reactions. Nat Chem, 3, 103-113.
[2]Qian, L. and Winfree, E. (2011) Scaling Up Digital Circuit Computation with DNA Strand
Displacement Cascades. Science, 332, 1196-1201.
[3]Wu, L., Shimada, N., Kano, A. and Maruyama, A. (2008) Poly(l-lysine)-graft-dextrancopolymer accelerates DNA hybridization by two orders. Soft Matter., 4, 744-747.
[4]Kim, W.J., Akaike, T. and Maruyama, A. (2002) DNA Strand Exchange Stimulated by
Spontaneous Complex Formation with Cationic Comb-Type Copolymer. Journal of the American
Chemical Society, 124, 12676-12677.
[5]Maruyama, A., Katoh, M., Ishihara, T. and Akaike, T. (1997) Comb-Type Polycations
Effectively Stabilize DNA Triplex. Bioconjugate Chemistry, 8, 3-6.