1. Intelligent DNA Chips: Logical Operation of Gene Expression Profiles on DNA Computers Ji Yoon Park Dept. of Biochem Hanyang University Yasubumi Sakakibara, Akira Suyama Genome Informatics 11: 33-42(2000)

2. Abstract 1. By combining with the DNA Coded Number(DCN) 1. By combining with the DNA Coded Number(DCN) method, we implement universal DNA chips which not method, we implement universal DNA chips which not only detect gene expression but also find logical formula only detect gene expression but also find logical formula of gene expressions. of gene expressions. 2. Advantage: - More quantitative analysis of gene expression profiles - More quantitative analysis of gene expression profiles and the logical operations. and the logical operations.

3. Object  Intelligent DNA chip and the DCN method allow us more quantitative analyses of gene expression profiles and the logical operations

4. DNA microarray 1. DNA microarray - The massive parallelism to enable to simultaneously - The massive parallelism to enable to simultaneously detect the expressions for a large number of genes detect the expressions for a large number of genes - Application: gene discovery/ disease diagnosis - Application: gene discovery/ disease diagnosis 2. DNA computing: Boolean functions on DNA strands 2. DNA computing: Boolean functions on DNA strands - Sakakibara: - Sakakibara: - DNF formula to a DNA strand, - DNF formula to a DNA strand, - evaluate the encoded DNF formula for a truth-value assignment - evaluate the encoded DNF formula for a truth-value assignment by using hybridization and primer extension with DNA pol by using hybridization and primer extension with DNA pol - Suyama: DNA Coded Number(DCN) - Suyama: DNA Coded Number(DCN) 1) genome information is first converted into data expressions 1) genome information is first converted into data expressions in DCNs using a conversion table written with DNA in DCNs using a conversion table written with DNA 2) DCN-encoded genome information analyzed with a power of 2) DCN-encoded genome information analyzed with a power of the massive parallelism of DNA computing the massive parallelism of DNA computing 3) The results of the analysis are finally obtained by reading out a 3) The results of the analysis are finally obtained by reading out a sequence of DCNs sequence of DCNs

5. DNA Coded Number(DCN) -Molecular arithmetic numbers by DNA base sequences chosen from a set of orthonormal DNA base seq -Orthonormal DNA seq: : Uniform melting temp. & no mishybridization or : Uniform melting temp. & no mishybridization or folding folding -Associated with expressed or unexpressed genes are generated using DNA molecular reaction.

6. A DNA chip with logical operations executable (A ∧ B) V C in the figures means: (A ∧ B) V C in the figures means: if the gene A is expressed and the gene B is expressed or if the gene C is not expressed, the formula is satisfied. if the gene A is expressed and the gene B is expressed or if the gene C is not expressed, the formula is satisfied. * ∧ : “ and ” operation * ∧ : “ and ” operation * V : “ or ” operation * V : “ or ” operation

7. cDNA Microarray scheme

8. Oncogene 18, 3666-3672(1999)

10. 1. mRNA preparation and cDNA synthesis 1. mRNA preparation and cDNA synthesis 2. Expressed genes: 2. Expressed genes: - the truth-value of a Boolean variable for the gene becomes 1. - the truth-value of a Boolean variable for the gene becomes 1. 3. Unexpressed genes: 3. Unexpressed genes: - the truth-value of a Boolean variable for the gene becomes 0. - the truth-value of a Boolean variable for the gene becomes 0. 4. DCN seqs are simultaneously applied to a DNA chip with DNA 4. DCN seqs are simultaneously applied to a DNA chip with DNA strands encoding Boolean formulae strands encoding Boolean formulae 5. The complementary marker sequences fluorescently tagged are 5. The complementary marker sequences fluorescently tagged are applied to the DNA chip after the logical evaluation and annealed applied to the DNA chip after the logical evaluation and annealed to marker in the DNA chip which remain single-stranded. to marker in the DNA chip which remain single-stranded. 6. * Color: truth-value of the Boolean formula at the element = 1 * No colar: = 0 * No colar: = 0

11. Intelligent DNA chip The intensity of the fluorescence at each element * The intensity of the fluorescence at each element - proportional to the expression level of the genes in the sample - proportional to the expression level of the genes in the sample - satisfiability level of the Boolean formula at the element with the - satisfiability level of the Boolean formula at the element with the gene expression pattern gene expression pattern ( x 1 ∧ ￢ x 2 ) ∨ (x 3 ∧ ￢ x 4 ) = 0 (: not satisfied); ds DNA No color ( x 1 ∧ ￢ x 2 ) ∨ (x 3 ∧ ￢ x 4 ) = 0 (: not satisfied); ds DNA No color ( x 1 ∧ ￢ x 2 ) ∨ (x 3 ∧ ￢ x 4 ) = 1 (: satisfied); ss DNA color ( x 1 ∧ ￢ x 2 ) ∨ (x 3 ∧ ￢ x 4 ) = 1 (: satisfied); ss DNA color - More marker subseqs in the formula remain single stranded, - More marker subseqs in the formula remain single stranded, there exist more terms which satisfied with the expression pattern there exist more terms which satisfied with the expression pattern - More complementary marker seqs fluorescently tagged are - More complementary marker seqs fluorescently tagged are annealed and the element shows the fluorescent color with greater annealed and the element shows the fluorescent color with greater level level

12. Applications Intelligent DNA chip - Logical inference for such diagnosis based on detected gene expression patterns - Logical inference for such diagnosis based on detected gene expression patterns - detect disease-related genes - detect disease-related genes - differential expression analysis - differential expression analysis : more easy and precisely realized : more easy and precisely realized

13. To detect specific genes using two different samples 1)We prepare two DCNs which represent two Boolean variables say “ A” and “ B”, for a gene expression in the target sample and the same gene expression in the other sample, and implement DNA chip with a probe for (A ∧ B) 2) By applying those samples, if the (A ∧ B) is found satisfied, we conclude the gene is expressed in the target sample and not expressed in the other sample, and hence the gene is specific to the target sample

14. Conclusion Intelligent DNA chip 1.By combining DNA chips with the DNA-computing method for representing and evaluating Boolean functions and the DCN method 1.By combining DNA chips with the DNA-computing method for representing and evaluating Boolean functions and the DCN method 2. Detect gene expression/ Find logical formula of gene 2. Detect gene expression/ Find logical formula of gene expression expression 3. Quantitative analysis of gene expression profiles using the intensity of the fluorescence at each element 3. Quantitative analysis of gene expression profiles using the intensity of the fluorescence at each element 4. Model gene regulation networks 4. Model gene regulation networks