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Formal Notation for DNA Molecules: A Comprehensive PhD Talk by Rudy van Vliet

On September 15, 2004, Rudy van Vliet presented a PhD talk at the LIACS, Leiden University, discussing a formal notation for DNA molecules, emphasizing the significance of DNA expressions in both genetic information and computer science. Key topics included complementarity of DNA strands, secondary structures like hairpin loops, and the implications of nicks and gaps in DNA configurations. This talk also addressed minimal DNA expressions, offering insights into their characterization and construction, along with the potential applications of DNA computing theory.

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Formal Notation for DNA Molecules: A Comprehensive PhD Talk by Rudy van Vliet

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  1. Rudy van Vliet Leiden Institute of Advanced Computer Science Leiden University DNA Expressions A formal notation for DNA molecules LIACS PhD talk September 15, 2004

  2. A C G T A A C T A G T C G A T C G A T T Building blocks A A C C A A T T G G C C A A T T T T G A T C G A T C A G C T A A T T G G T T A A C C G G T T A A Complementarity Strand s Perfect double stranded DNA C A G T G T C A Upper strand Lower strand Same molecule DNA Genetic information

  3. DNA and computer science Evolutionary algorithms DNA computing theory - splicing practice - Hamiltonian path problem

  4. A C A T G C A T T G T A C G T A A C A T G C A T Secondary structure: Hairpin loop: T G A A C C G C G G C A T A C A A T T T G T A C G T A A Why notation? Perfect double stranded molecule:

  5. Why notation?

  6. A C A T G C A T T G T A C G T A A C A T G T A G C T A A T C G T G T A C A T G T G C A C A T G C T G T C G T A Gaps and nicks no gaps, no nicks gaps, no nicks gaps, lower nicks no gaps, upper nick gap, upper nick, lower nick

  7. A G T C ………  ……… C A T G T G C ………       T T C C AT AT      G G G T A T C     Abstract DNA molecules bases + operators DNA expressions minimal DNA expressions

  8. A G T C ………  ……… C A T G T G C ………       T T C C AT AT      G G G T A T C     Abstract (2) DNA molecules bases + operators DNA expressions normal form DNA expression

  9. N-words ACATGCAT

  10. AT lower nicks may appear removes upper nicks creates upper strands connects upper strands of arguments    A A C G A C T G C T T C T G C G G C A T A G  DNAexpressions

  11. AT upper nicks may appear removes lower nicks creates lower strands connects lower strands of arguments T T   A C G C T A C A T C G T C A G T T G C A A T A T C C G C G T G A T T A A C G G C T G G A C G  DNAexpressions 

  12. A C A T G C A T AT T G T A C G T A connects new nucleotides to neighbours complements argument T T T   T C A T C A G G T A C C C C T A G C C G T A T G A T A C C A T C T A G G C T G G C G G G T A G A A G C T T A G G C A C T  DNAexpressions  C 

  13. A A C C A A T T G G C C A A T T AT T T G G T T A A C C G G T T A A T T T           A A C C T T T C C A T A G C T A A C T G A C G T A T C C G C G A T C  T G G G C A G C G A A G C T T G A T G G T A G G C C   DNAexpressions  C T C AT G C A T

  14. A A C C A A T T G G C C  A A T T AT T T G G T T A A C C G G T T A A  T T   T         T AT C A C T G G A C C T A C T G C C A C T T A G C T C C T G A T A T A A  G G T C A A G C G T G C T A A G C C G G G T G G T A DNAexpressions C  C G C A T

  15. A A C C A A T T G G C C A A T T AT T T G G T T A A C C G G T T A A T T T           A A C C T T T C C A T A G C T A A C T G A C G T A T C C G C G A T C  T G G G C A G C G A A G C T T G A T G G T A G G C C   DNAexpressions  C T C AT G C A T

  16. A C A T G C A T T G T A C G T A A C A T G T A G C T A A T C G T G T A C A T G T G C A C A T G C T G T C G T A Expressible DNA molecules A DNA molecule is expressible, if and only if it contains nicks in at most one strand.     

  17. A C A T G C A T T G T A C G T A ACATGC AT              Equivalent DNA expressions T C AT G C A T

  18. Introduction of DNA expressions For each expressible DNA molecule, Number of minimal DNA expressions Characterization of minimal DNA expressions Normal form      www.liacs.nl/home/rvvliet/mindnaexpr.html (in terms of Catalan numbers) Conclusions we can construct the minimal DNA expressions More info:

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