Using the a* algorithm to build dna nanostructures

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Chapter 1

Introduction and Background

1.1 Related Work and Project Concept

In the late 1980s Nadrian C. Seeman at New York University, founded the .eld of Structural DNA Nanotechnology [ACS01]. Since then many other labs have started exploring the possibilities of using DNA as structural material.

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Various di.erent DNA machines have been constructed [NNT02]. Examples of these machines include; the “tweezers” [NNT01], the “walker” [NAN01], the “rickettsia motif” [NNT03], the “lockbox” [NAT01], and the proposed “stack” [CHA01] should also be mentioned. Some of the structures present in these machines have been replicated using the resulting software from this project.

Some software that aim to design DNA structures include; caDNAno [CAD01], NanoEngineer-1 [NEN01], NUPACK [NUP01], SARSE [SAR01], and UNAFold [NAR01]. Most of these software packages are used for designing DNA origami structures, a concept discovered by Paul Rothemund [ROT01] [NAT02].

The software in this project was written based on Jessica P. Changs topological modelling of DNA [CHA01]. This abstraction of DNA behavior lay the foundation for a technique to perform quick test tube simulations of mixing DNA strands. The second objective of the software is to sequence the construction of a designed DNA structure. By mixing DNA strands in a test tube they will combine and attach to each other in particular con.gurations. Depending on what DNA strands are mixed, what quantities, and in which order, the resulting DNA structures will be di.erent.

Starting with an empty test tube, referred to here as a vessel, di.erent fuel strands can be added to produce vessels with di.erent contents. In the process of developing a method for planing the construction of designed DNA structures, a vessel can be seen as a node in a directed graph, and the resulting vessels from adding fuel strands, can be seen as neighboring nodes with edges in the direction from the original node, to the neighboring nodes.

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The idea for the objective of constructing DNA structures, was to use the A* algorithm to search this state space of vessels. A state could be de.ned as a vessel containing the designed DNA structure. The heuristic function needed for the A* algorithm would then be developed to estimate the number of additional fuel strands that would have to be added in order to produce a vessel containing the goal structure.

1.2 Introduction to DNA

DNA consists of four di.erent bases; Adenine, Guanine, Cytosine,and Thymine, commonly referred to as A, G, C, T [NHG01]. A base liked to a sugar is called a nucleoside. The backbone of the DNA strand is made from nucleosides joined together by phosphate. The phosphate form asymmetric bonds between the third and .fth carbon atoms of the adjacent sugar rings.

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