Molecular Immnuocomputing with Application to Alphabetical Pattern Recognition Mimics the

Characterization of ABO Blood Type

Su Dong Kim2 , Ki-Roo Shin1 & Byoung-Tak Zhang1,2*

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 inPeptide 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

Operator Operation

WTransition

{C ↔ T}, {A ↔ G}

XMatched-transition

{A ↔ T}, {C ↔ G}

YMismatched-transversion

{A ↔ C}, {G ↔ T}

ZBack-mutation

(null mutation)

Designing the Peptide Sequences

a t c c c t t

t c g g g c t

t c g g g c t

t c g g g c t

t c g g g c t

t c g g g c t

t t c c c t t

1 2 3 4 5 6 7

8 9 10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49“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 (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)

Classes of Capture Molecules for Protein Microarrays

Sandwich immunoassay

(Templin et al. , 2002)

Conclusion

Peptide computing Immunocomputing

Alternative toDNA computing

based onMathematical model

Biomolecule → Computation Computation → 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 MECproject, and the NRL Program from Korean Ministry of Science &Technology.The ICT at Seoul National University provided research facilitiesfor this study.