Errors in DNA Self-Assembly by Synthesized Tile Sets

This paper presents a study of errors that occur in DNA self-assembly using synthesized tile sets for template manufacturing. It is shown that due to the reduced size, aggregates assembled by a synthesized tile set are not error-free as those assembled by maximum-sized (referred to as a trivial tile set) as well asnon-synthesized tile sets. Compared with non-synthesized tile sets, aggregates assembled using synthesized tile sets also have a higher error rate at high tile concentration, but they exhibit a lower rate at low tile concentration. In this paper, it is also shown that errors in synthesized tile sets tend to appear in clusters. This is very different from non-synthesized tile sets of non-maximum size in which growth errors are mostly random in nature. These findings are discussed and evaluated for nano manufacturing (such as for template self-assembly of a QCA circuit).

[1]  Wenchuang Hu,et al.  High-resolution electron beam lithography and DNA nano-patterning for molecular QCA , 2005, IEEE Transactions on Nanotechnology.

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

[3]  Robert D. Barish,et al.  Three-helix bundle DNA tiles self-assemble into 2D lattice or 1D templates for silver nanowires. , 2005, Nano letters.

[4]  Erik Winfree.  DNA Computing by Self-Assembly , 2003 .

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

[6]  Hao Yan,et al.  Programmable DNA self-assemblies for nanoscale organization of ligands and proteins. , 2005, Nano letters.

[7]  Jing Huang,et al.  Design and Test of Digital Circuits by Quantum-Dot Cellular Automata , 2007 .

[8]  Michael T. Niemier,et al.  Molecular QCA design with chemically reasonable constraints , 2008, JETC.

[9]  Wenchuang Hu,et al.  Electron beam lithography and liftoff of molecules and DNA rafts , 2004, 4th IEEE Conference on Nanotechnology, 2004..

[10]  Erik Winfree,et al.  Self-healing Tile Sets , 2006, Nanotechnology: Science and Computation.

[11]  J. Reif,et al.  Electronic nanostructures templated on self-assembled DNA scaffolds , 2004 .

[12]  Erik Winfree,et al.  Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly , 2003, DNA.

[13]  Xiaojun Ma,et al.  Synthesis of Tile Sets for DNA Self-Assembly , 2008, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

[14]  Michail G. Lagoudakis,et al.  2D DNA self-assembly for satisfiability , 1999, DNA Based Computers.

[15]  Erik Winfree,et al.  Two computational primitives for algorithmic self-assembly: copying and counting. , 2005, Nano letters.