Abstract
The design of DNA sequences is a key problem for
implementing molecular self-assembly with nucleic acid
molecules. These molecules must meet several physical,
chemical and logical requirements, mainly to avoid
mishybridization. Since manual selection of proper
sequences is too time-consuming for more than a handful
of molecules, the aid of computer programs is
advisable. In this paper two software tools for
designing DNA sequences are presented, the
DNASequenceGenerator and the DNASequenceCompiler. Both
employ an approach of sequence dissimilarity based on
the uniqueness of overlapping subsequences and a graph
based algorithm for sequence generation. Other sequence
properties like melting temperature or forbidden
subsequences are also regarded, but not secondary
structure errors or equilibrium chemistry. Fields of
application are DNA computing and DNA-based
nanotechnology. In the second part of this paper,
sequences generated with the DNASequenceGenerator are
compared to those from several publications of other
groups, an example application for the
DNASequenceCompiler is presented, and the advantages
and disadvantages of the presented approach are
discussed.
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