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

Introduction DNA computing Peptide computing vs.

Four Types of Noncovalent Bonds in Peptide Computing

Structure of Antibody with Its Antigen

Molecular Immunocomputing Mimics the Characterization of ABO Blood Type

The ABO Blood Grouping System

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

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

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

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)

Designing the Peptide Sequences atccctt tcgggct tcgggct tcgggct tcgggct tcgggct ttccctt “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

The Universal Genetic Code

Hapten-Carrier Conjugation & Immunization

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

Discussion (a) Structures of the peptide CTP3 (VEVPGSQHIDSQKKA) (a), PS1 (HQLDPAFGANSTNPD) (b), SHaPrP ( ; 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)

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

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

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.