DNASequenceGenerator: A Program for the construction of DNA sequences Udo Feldkamp, Sam Saghafi, Wolfgang Banzhaf, Hilmar Rauhe DNA7 pp. 179-188 Summarized.

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DNASequenceGenerator: A Program for the construction of DNA sequences Udo Feldkamp, Sam Saghafi, Wolfgang Banzhaf, Hilmar Rauhe DNA7 pp Summarized by Dongmin Kim

© 2001 SNU CSE Artificial Intelligence Lab (SCAI) Introduction The main purpose for designing DNA sequences:  Find a set of sequences as dissimilar as possible, include complementary sequences.  avoid non-specific hybridizations.  Control the thermodynamic properties of the sequences  Regard other constraints given by the application.

© 2001 SNU CSE Artificial Intelligence Lab (SCAI) Theoretical background(1) The concept of uniqueness  n b -unique if any subsequence in the pool of length n b if unique  Uniqueness 1-(n b -1)/n s, a ratio to measure how much of a set of sequences of length n s is unique.  Example  9mers these are 6-unique have at most 5 subsequent common subsequence and a uniqueness of 44%

© 2001 SNU CSE Artificial Intelligence Lab (SCAI) Theoretical background(2) The number of base strands of length n b is The number of base strands that can be used in the generation process is The maximum number of sequences is Further requirements such as GC-ratio, melting temperature, the exclusion of long guanine subsequences or of start codons decrease the yield.

© 2001 SNU CSE Artificial Intelligence Lab (SCAI) DNA Sequence Generator The user can  Import or manually add existing or strictly required sequences  Import or manually add sequence templates  Generate sequences de novo  Use the DNASequenceGenerator as a T m calculator  Estimating the melting temperature can be chosen in Wallace rule, GC-% formula, nearest-neighbor method

© 2001 SNU CSE Artificial Intelligence Lab (SCAI) Result In silico In vitro  Generate oligonucleotides for parallel overlap assembly, and tested in vitro  Sequences have restriction sites at specified locations, and a GC ratio of 50%

© 2001 SNU CSE Artificial Intelligence Lab (SCAI) DNASequenceCompiler Sibling tool of DNASequenceGenerator  More suited for sticky-end design.  Designed to translate formal grammars directly into DNA molecules representing the rules of the grammar  Provides an interface for the programmable self- assembly of molecules

© 2001 SNU CSE Artificial Intelligence Lab (SCAI) Conclusion A software tool for the design of DNA oligomers useful for DNA computation. The design of sophisticated DNA structures, such as cubes or double- or triple-crossover molecules will require a more specialized program.