Algorithmic Pot Generation: Algorithms for the Flexible-Tile Model of DNA Self-Assembly

Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA molecules that bond to each other at complementary cohesive ends. One practical question is: given a target nanostructure, what is the optimal set of DNA molecules that assemble such a structure? We use a flexible-tile graph theoretic model to develop several algorithmic approaches, including a integer programming approach. These approaches take a target undirected graph as an input and output an optimal collection of component building blocks to construct the desired structure.

• Publication year

  2024

• Venue

  Unknown venue

• Publication date

  2024-07-31

• Fields of study

  Biology, Mathematics, Computer Science

• Identifiers
  arXiv 2408.00192
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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  2018cited by this paper
• Physical principles for DNA tile self-assembly.

  2017cited by this paper
• Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs

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• Molecular robots guided by prescriptive landscapes

  2010cited by this paper
• A Bipedal DNA Brownian Motor with Coordinated Legs

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• Constructing novel materials with DNA

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• Spectrum of a Pot for DNA Complexes

  2006cited by this paper
• DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires

  2003cited by this paper
• DNA branched junctions.

  1994cited by this paper
• Molecular computation of solutions to combinatorial problems.

  1994cited by this paper
• Assembly and characterization of five-arm and six-arm DNA branched junctions.

  1991cited by this paper

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