Intelligent DNA Chips Logical Operation of Gene Expression

Intelligent DNA Chips: Logical Operation of Gene Expression Profiles on DNA Computers Yasubumi Sakakibara, Akira Suyama Genome Informatics 11: 33 -42(2000) Dong-yeon, Cho

Introduction l Intelligent DNA chip makes use of ¨ Massive parallelism of DNA chip(Microarray) ¨ Methods to encode any DNF Boolean formula to a DNA strand[Y. Sakakibara, 2000] ¨ DNA Coded Number(DCN) method for processing genome information[Suyama et al, 2000] l DNA chip with information processing abilities

DNA Coded Number l DNA molecules representing numbers chosen from a set of orthonormal DNA sequences ¨ Orthonormal DNA sequence: have uniform melting temperature and no mishybridization or folding potential l Associated with expressed or unexpressed genes and generated by DNA molecular reaction

Generation of DCN Numbers Encoding genes with DCN Target transcript i Amplifying DCN Generate DCN for expressed and unexpressed genes

Evaluating Boolean Formulae on DNA Strands l Boolean variables correspond to the gene expression ¨ If a gene is expressed, associated variable has truth value 1, else associated variable has 0 l means if both gene A is expressed and B is not expressed, or if both gene C is not expressed and D is expressed then the formula is satisfied

Evaluation of Formula(False) Makes the formula false Annealing Primer extension with DNA polymerase

Evaluation of Formula(True) Makes the formula true Annealing Primer extension with DNA polymerase

An Intelligent DNA Chip Encoding DNA chip with logical formula

Applications l Logical inference for such diagnosis based on detected gene expression patterns ¨ detect disease-related genes ¨ differential expression analysis < more easy and precisely realized

Conclusion By combining DNA chips with the DNA-computing method for representing and evaluating Boolean functions and the DCN method ¨ Detect gene expression/ Find logical formula of gene expression ¨ Quantitative analysis of gene expression profiles using the intensity of the fluorescence at each element ¨ Model gene regulation networks