1. Molecular Immnuocomputing with Application to Alphabetical Pattern Recognition Mimics the Characterization of ABO Blood Type Su Dong Kim 2, Ki-Roo Shin 1 & Byoung-Tak Zhang 1,2* 1 School of Computer Science & Engineering, Seoul National University, Seoul, Korea 2 Interdisciplinary Program in Cognitive Science, Seoul National University, Seoul, Korea

2. Introduction DNA computing Peptide computing vs.

3. Four Types of Noncovalent Bonds in Peptide Computing

4. Structure of Antibody with Its Antigen

5. Molecular Immunocomputing Mimics the Characterization of ABO Blood Type

6. The ABO Blood Grouping System

7. The Structure of Terminal Sugars in the A, B, & O Blood Antigens (Gal; Galactose, GlcNAc; N-acetylglucosamine, Fuc; Fucose, and GalNAc; N-acetylgalactosamine)

8. Nucleotide Sequences of ABO Alleles Identified by PCR-SSCP Analysis (Ogasawara et al., 1996)

9. Methods Designing the peptide sequences Purifying the corresponding antibodies Preparation of protein microarray chips

10. Four Kinds of DNA Code Operators OperatorOperation W Transition {C ↔ T}, {A ↔ G} X Matched-transition {A ↔ T}, {C ↔ G} Y Mismatched-transversion {A ↔ C}, {G ↔ T} Z Back-mutation (null mutation)

11. Designing the Peptide Sequences atccctt tcgggct tcgggct tcgggct tcgggct tcgggct ttccctt 1234567 891011121314 15161718192021 22232425262728 29303132333435 36373839404142 43444546474849 “O”- DNA template sequence: 5’- a tcc ctt tcg ggc ttc ggg ctt cgg gct tcg ggc ttc ggg ctt tcc ctt – 3’ “O”- RNA transcript sequence: 3’ – ugu agg gaa agc ccg aag ccc gaa gcc cga agc ccg aag ccc gaa agg gaa – 5’ “O”- peptide sequence: HOOC - * C G K R A E P K P K P S R A E P K G K -NH2

12. The Universal Genetic Code

13. Hapten-Carrier Conjugation & Immunization

14. Preparation of Protein Microarray Chips (Haab et al., 2001a) (Zhu & Snyder, 2003)

15. Discussion (a) Structures of the peptide CTP3 (VEVPGSQHIDSQKKA) (a), PS1 (HQLDPAFGANSTNPD) (b), SHaPrP (104-113 ; KPKTNMKHMA) (c), and peptide with antigen binding site (d). [(a), (b), and (c): drawed by the Swiss-PdbViewer (Guex & Peitsch, 1997); (d): adapted from Lescar et al., 1991.] (b) (c)(d)

16. Classes of Capture Molecules for Protein Microarrays Sandwich immunoassay (Templin et al., 2002)

17. Conclusion Peptide computingImmunocomputing Alternative to DNA computing based on Mathematical model Biomolecule → ComputationComputation → Biomolecule = Molecular Immunocomputing (?)

18. Acknowledgments This research was supported in part by the Ministry of Education & Human Resources Development under the BK21-IT Program, The Ministry of Commerce, Industry and Energy through the MEC project, and the NRL Program from Korean Ministry of Science & Technology. The ICT at Seoul National University provided research facilities for this study.