Polar organic solvents accelerate the rate of DNA strand replacement reaction.

Herein, we report a novel strategy to accelerate the rate of DNA strand replacement reaction (DSRR) by polar organic solvents. DSRR plays a vital role in DNA nanotechnology but prolonged reaction time limits its further advancement. That is why it is extremely important to speed up the rate of DSRR. In this work, we introduce different polar organic solvents in both simple and complicated DSRR systems and observe that the rate constant is much more than in aqueous buffer. The rate acceleration of DSRR by polar organic solvents is very obvious and we believe that this strategy will extend the application of DNA nanotechnology in future.

[1]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[2]  D. Stefanovic,et al.  Deoxyribozyme-based half-adder. , 2003, Journal of the American Chemical Society.

[3]  Adam T Woolley,et al.  Polymerase chain reaction based scaffold preparation for the production of thin, branched DNA origami nanostructures of arbitrary sizes. , 2009, Nano letters.

[4]  Ying Wang,et al.  Analogic China map constructed by DNA , 2006 .

[5]  Brendan D. Smith,et al.  Assembly of DNA-functionalized nanoparticles in alcoholic solvents reveals opposite thermodynamic and kinetic trends for DNA hybridization. , 2010, Journal of the American Chemical Society.

[6]  Weihong Tan,et al.  A Single DNA Molecule Nanomotor , 2002 .

[7]  Mingdong Dong,et al.  DNA origami design of dolphin-shaped structures with flexible tails. , 2008, ACS nano.

[8]  N. Seeman.  DNA nanotechnology: novel DNA constructions. , 1998, Annual review of biophysics and biomolecular structure.

[9]  Chunhai Fan,et al.  Sequence-specific detection of femtomolar DNA via a chronocoulometric DNA sensor (CDS): effects of nanoparticle-mediated amplification and nanoscale control of DNA assembly at electrodes. , 2006, Journal of the American Chemical Society.

[10]  J. Bonner,et al.  A method for the hybridization of nucleic acid molecules at low temperature. , 1967, Biochemistry.

[11]  Shawn M. Douglas,et al.  Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.

[12]  Luca Cardelli,et al.  Design and analysis of DNA strand displacement devices using probabilistic model checking , 2012, Journal of The Royal Society Interface.

[13]  A. Saghatelian,et al.  DNA-based photonic logic gates: AND, NAND, and INHIBIT. , 2003, Journal of the American Chemical Society.

[14]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[15]  Lloyd M. Smith,et al.  DNA computing on surfaces , 2000, Nature.

[16]  B. McConaughy,et al.  Nucleic acid reassociation in formamide. , 1969, Biochemistry.

[17]  N. Seeman.  Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[18]  N. Seeman,et al.  A Proximity-Based Programmable DNA Nanoscale Assembly Line , 2010, Nature.

[19]  G. Seelig,et al.  Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.

[20]  G Sczakiel,et al.  Dissociation of long-chain duplex RNA can occur via strand displacement in vitro: biological implications. , 1996, Nucleic acids research.

[21]  P. Yin,et al.  A DNAzyme that walks processively and autonomously along a one-dimensional track. , 2005, Angewandte Chemie.

[22]  N. Pierce,et al.  A synthetic DNA walker for molecular transport. , 2004, Journal of the American Chemical Society.

[23]  Hao Yan,et al.  DNA tile based self-assembly: building complex nanoarchitectures. , 2006, Chemphyschem : a European journal of chemical physics and physical chemistry.

[24]  M. Meyyappan,et al.  Carbon Nanotube Nanoelectrode Array for Ultrasensitive DNA Detection , 2003 .

[25]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[26]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[27]  N. Seeman,et al.  An immobile nucleic acid junction constructed from oligonucleotides , 1983, Nature.

[28]  A. Condon,et al.  Demonstration of a word design strategy for DNA computing on surfaces. , 1997, Nucleic acids research.

[29]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

[30]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[31]  Juewen Liu,et al.  Fast molecular beacon hybridization in organic solvents with improved target specificity. , 2010, The journal of physical chemistry. B.

[32]  Xi Chen,et al.  Expanding the rule set of DNA circuitry with associative toehold activation. , 2012, Journal of the American Chemical Society.

[33]  Nicolas H Voelcker,et al.  Sequence-addressable DNA logic. , 2008, Small.

[34]  Tao Li,et al.  Potassium-lead-switched G-quadruplexes: a new class of DNA logic gates. , 2009, Journal of the American Chemical Society.

[35]  Ruojie Sha,et al.  A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.

[36]  Erik Winfree,et al.  Molecular robots guided by prescriptive landscapes , 2010, Nature.

[37]  N. Seeman,et al.  Ligation of DNA Triangles Containing Double Crossover Molecules , 1998 .