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Design of DNA Sequences for Stable DNA Tile

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DNA tiles have played an indispensable role in DNA self-assembly, DNA Nanotechnology and DNA computation. In order to form stable DNA tiles, DNA sequences need to be optimized with some constraints. Winfree et al. have proposed a scoring system, which was based on some constraints, to optimize DNA sequences by changing a single base at a time randomly. In this paper, we proposed a randomly traversal algorithm to optimize DNA sequences. The proposed algorithm can do the same time's changes for each base of the sequence. This effectively excludes redundant base change steps, thereby reducing optimization time. Simulation results showed the practicality and validity of our algorithm.

Keywords: DNA SEQUENCES DESIGN; DNA TILE; RANDOMLY TRAVERSAL ALGORITHM; SEQUENCE OPTIMIZATION

Document Type: Research Article

Publication date: 01 June 2013

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  • Bionanoscience attempts to harness various functions of biological macromolecules and integrate them with engineering for technological applications. It is based on a bottom-up approach and encompasses structural biology, biomacromolecular engineering, material science, and engineering, extending the horizon of material science. The journal aims at publication of (i) Letters (ii) Reviews (3) Concepts (4) Rapid communications (5) Research papers (6) Book reviews (7) Conference announcements in the interface between chemistry, physics, biology, material science, and technology. The use of biological macromolecules as sensors, biomaterials, information storage devices, biomolecular arrays, molecular machines is significantly increasing. The traditional disciplines of chemistry, physics, and biology are overlapping and coalescing with nanoscale science and technology. Currently research in this area is scattered in different journals and this journal seeks to bring them under a single umbrella to ensure highest quality peer-reviewed research for rapid dissemination in areas that are in the forefront of science and technology which is witnessing phenomenal and accelerated growth.
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