DNA based arithmetic function: a half adder based on DNA strand displacement.

Biomolecular programming utilizes the reactions and information stored in biological molecules, such as proteins and nucleic acids, for computational purposes. DNA has proven itself an excellent candidate for building logic operating systems due to its highly predictable molecular behavior. In this work we designed and realized an XOR logic gate and an AND logic gate based on DNA strand displacement reactions. These logic gates utilize ssDNA as input and output signals. The XOR gate and the AND gate were used as building blocks for constructing a half adder logic circuit, which is a primary step in constructing a full adder, a basic arithmetic unit in computing. This work provides the field of DNA molecular programming with a potential universal arithmetic tool.

[1]  Hao Yan,et al.  Challenges and opportunities for structural DNA nanotechnology. , 2011, Nature nanotechnology.

[2]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[3]  F. Simmel.  Towards biomedical applications for nucleic acid nanodevices. , 2007, Nanomedicine.

[4]  Bernard Yurke,et al.  Using DNA to Power Nanostructures , 2003, Genetic Programming and Evolvable Machines.

[5]  Hao Yan,et al.  Designer DNA nanoarchitectures. , 2009, Biochemistry.

[6]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[7]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[8]  L. Marky,et al.  Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding. , 1993, Nucleic acids research.

[9]  E. Winfree,et al.  Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.

[10]  Hao Yan,et al.  Reconfigurable DNA origami to generate quasifractal patterns. , 2012, Nano letters.

[11]  Hao Yan,et al.  Controlled Nucleation and Growth of DNA Tile Arrays within Prescribed DNA Origami Frames and Their Dynamics , 2014, Journal of the American Chemical Society.

[12]  Mauro Ferrari,et al.  Nanomedicine--challenge and perspectives. , 2009, Angewandte Chemie.

[13]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[14]  G. Seelig,et al.  DNA as a universal substrate for chemical kinetics , 2010, Proceedings of the National Academy of Sciences.

[15]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[16]  Erik Winfree,et al.  An information-bearing seed for nucleating algorithmic self-assembly , 2009, Proceedings of the National Academy of Sciences.

[17]  R. Levine,et al.  DNA computing circuits using libraries of DNAzyme subunits. , 2010, Nature nanotechnology.

[18]  Luca Cardelli,et al.  A programming language for composable DNA circuits , 2009, Journal of The Royal Society Interface.

[19]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

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

[21]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[22]  A. Turberfield,et al.  DNA fuel for free-running nanomachines. , 2003, Physical review letters.

[23]  Hao Yan,et al.  Targeted cell-cell interactions by DNA nanoscaffold-templated multivalent bispecific aptamers. , 2011, Small.

[24]  Yan Liu,et al.  Three-input majority logic gate and multiple input logic circuit based on DNA strand displacement. , 2013, Nano letters.

[25]  Luca Cardelli,et al.  Programmable chemical controllers made from DNA. , 2013, Nature nanotechnology.

[26]  Ehud Shapiro,et al.  A library of programmable DNAzymes that operate in a cellular environment , 2013, Scientific Reports.

[27]  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 .

[28]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .