(C) 2002, SNU Biointelligence Lab, A Computer Scientist’s Guide to Molecular Biology Biointelligence Lab. Interdisciplinary Program in Cognitive Science, Seoul National University L. Kari et al., Soft Computing 5 (2001)

(C) 2002, SNU Biointelligence Lab, Outline Introduction The DNA molecule The natural information contents of DNA  Transcription  Editing  Translation Adleman’s in vitro experiment DNA as a computational tool

3 Biocomputing vs. Bioinformatics MolecularBiology ComputerScience Bioinformatics Molecular computing Biomolecular computing DNA computing

(C) 2002, SNU Biointelligence Lab, The DNA Molecule

(C) 2002, SNU Biointelligence Lab, DNA (deoxyribonucleic acid) Schrödinger (1944): What is Life?  Our genes must essentialy be an aperiodic crystal Watson & Crick (1953): Nature 25:  Molecular Structure of Nucleic Acids: A structure for deoxyribose nucleic acid  Nobel Prize, 1962.

6 DNA Structure (1) nucleotide

7 DNA Structure (2) ester bond Long and unbranched polymers formed by ester bonds between the 5’ phosphate (5’-P) and the 3’ hydroxyl (3’-OH) group of the sugar of the next.

8 DNA Structure (3) base pairing Complimentary base pairing accounts for the Chargaff’s rule (A=T, G=C).

9 DNA Structure (4) – double helix Watson-Crick complement

10 DNA Structure (5) – conformation The B-form is the common natural form, prevailing under physiological conditions of low ionic strength and high degree of hydration. The Z-form (Zigzag chain) is observed in DNA G-C rich local region. The A-form is sometimes found in some parts of natural DNA in presence of high concentration of cations or at a lower degree of hydration (<65%).

(C) 2002, SNU Biointelligence Lab, The Natural Information Content of DNA

12 Central Dogma

13 Replicaton (1) Each time a cell divides into two daughter cells, all the DNA molecule must be duplicated. Duplication of an old DNA molecule into two new DNA molecules is called Replication.

14 Replicaton (2) During replication, the DNA helix is unraveled and its two strands are separated. An area known as the replication bubble forms and progresses along the molecule in both direction. Then each DNA strand serves as a template for the synthesis of a new complementary strand. Each daughter DNA molecule is an exact copy of its parent molecule, consisting of one old and one new DNA strand. Thus the replication is semi-conservative

15 Transcription Scientists snap first 3-D pictures of the "heart" of the transcription machine.

16 Editing Capping PolyAdenylation RNA splicing

17 5’ Capping (1) There are three cap structures that have been identified: Cap 0, Cap 1 and Cap 2. The structures all have the methylated guanine but differ in the extent of methylation of the ribose moiety of the first and second position of the RNA chain.

18 5’ Capping (2) 3 functions of 5’ cap  protection of the RNA from degradation  translatability  transport from the nucleus to the cytoplasm

19 Polyadenylation (1) Polyadenylation mechanism involves following steps: 1. The cutting of the RNA chain at a particular site 2. The addition of the poly [A] to the 3' end of the pre-mRNA 3. The degradation of the remainder of the RNA transcript

20 Polyadenylation (2) Two functions for poly [A] on mRNA; 1. Protection 2. Translatability

21 RNA Splicing (1)

22 RNA Splicing (2)

23 RNA Splicing (3)

24 Translation (1)

25 Translation (2) tRNA structure

26 Translation (3)

27 Translation (4) Initiation

28 Translation (5) Elongation

29 Translation (6) Termination

(C) 2002, SNU Biointelligence Lab, The First DNA Computing Method L. M. Adleman, Molecular Computation of Solutions to Combinatorial Problems, Science, 266: , 1994

(C) 2002, SNU Biointelligence Lab, First special DNA computer Special problem: given N points, find a path visiting each and every point only once, and starting and ending at a given locations. (Hamiltonian path problem) Solved with a DNA computer by Leonard Adleman in 1994 for N=7 Basic approach: code each point as an 8 unit DNA string, code each possible path, allow DNA bonding, suppress DNA with incorrect start/end points.

(C) 2002, SNU Biointelligence Lab, Hamiltonian Path Problem The Hamiltoian path problem: as the number of cities grows, even supercomputers have difficulty finding the path

(C) 2002, SNU Biointelligence Lab, Adleman’s Molecular Computer: A Brute Force Method Each city (vertex) is represented by a different sequence of nucleotides (6 here, but Adleman used 20). A DNA linker (edge) joining two city (vertex) strands.

(C) 2002, SNU Biointelligence Lab, Encoding (Basic Concept) AGCT TAGG P 1A P 1B TAGG CATG P 2A P 2B CGAT CGAA P 3A P 3B P 1B P 3A P 1B P 2A ATCC TACC ATCC GCTA

35 Procedure Generate random paths through the graph Keep only those paths that begin with v in and end with v out If the graph has n vertices, then keep only those paths that enter exactly n vertices If any paths remain, say “Yes”; otherwise, say “No.” Hybridization & Ligation PCR with v in and v out Gel electrophoresis Gel electrophoresis & Sequecing Keep only those paths that enter all of the vertices of the graph at least once. Antibody bead separation With v i

(C) 2002, SNU Biointelligence Lab, AGCTTAGG ATGGCATG ATCCTACC Vertex 1Vertex 2 Edge 1  2 Step 1 : Hybridization AGCTTAGGATGGCATG ATCCTACC AGCTTAGG ATCCTACC Step 2 : Ligation AGCTTAGGATGGCATGGAATCCGATGCATGGC TCGAATCCACGTACCG Vertex 1 ATGGCATG Vertex 4 Step 3 : PCR 56 bp 16 bp Step 4 : Gel Electrophoresis AGCTTAGGATGGCATGGAATCCGA… TCGAATCC Bead for vertex 1 Step 5 : Magnetic Bead Affinity Separation

(C) 2002, SNU Biointelligence Lab, HPP... ATG ACG TGC CGA TAA GCA CGT Solution PCR (Polymerase Chain Reaction) ATGTGCTAACGAACG ACGCGAGCATAAATGTGCCGT TAAACG CGACGT TAAACGGCAACG... CGACGTAGCCGT... ACGCGAGCATAAATGTGCCGT ACGCGTAGCCGT ACGCGT... ACGGCATAAATGTGCACGCGT ACGCGAGCATAAATGCGATGCCGT ACGCGAGCATAAATGTGCCGT... ACGCGAGCATAAATGTGCCGT Decoding Ligation Encoding Gel Electrophoresis Affinity Column ACGCGAGCATAAATGTGCACGCGT ACGCGAGCATAAATGCGATGCACGCGT ACGCGAGCATAAATGTGCACGCGT ACGCGAGCATAAATGCGATGCACGCGT Node 0 : ACGNode 3 : TAA Node 1 : CGANode 4 : ATG Node 2 : GCANode 5 : TGC Node 6 : CGT

(C) 2002, SNU Biointelligence Lab, DNA finds a solution! A Hamiltonian path with all vertices included is isolated and recovered

(C) 2002, SNU Biointelligence Lab, DNA as a Computational Tool

40 DNA Memory A string composed of a series of four types of units (nucleotides), DNA may be viewed as logic memory or gate. Number System (Base 4): Nucleotide A C T G Complement Nucleotide DNA binding process Two strings of DNA are bonded by paired nucleotides A-C and C-G which may be considered as complements. Example: Number TTACAG has a complement AATGTC

(C) 2002, SNU Biointelligence Lab, DNA Memory DNA memory strands a t c g g t c a t a g c a c t 000 a t c g g t c a t a 101 t a g c c c g t g a Writing : make DNA sequences Reading : hybridization and readout

(C) 2002, SNU Biointelligence Lab, DNA Operators The bio-lab technology. Hybridization Ligation Polymerase Chain Reaction (PCR) Gel electrophoresis Affinity separation (Bead) Enzymes: restriction enzyme…

(C) 2002, SNU Biointelligence Lab, Hybridization & Ligation Hybridization  base-pairing between two complementary single-strand molecules to form a double stranded DNA molecule Ligation  Joining DNA fragments together Solution generation step!

(C) 2002, SNU Biointelligence Lab, DNA Hybridization & Ligation CGTACCTTAGGCT AGCTTAGGATGGCATGGAATCCGATGCATGGC CGTACCTTAGGCT AGCTTAGGATGGCATGGAATCCGATGCATGGC CGTACCTTAGGCT AGCTTAGGATGGCATGGAATCCGATGCATGGC CGTACCTTAGGCT AGCTTAGGATGGCATGGAATCCGATGCATGGC + + Ligation Hybridization Dehybridization

(C) 2002, SNU Biointelligence Lab, PCR (Polymerase Chain Reaction) Mullis: Nobel Prize (1993) Amplifies (produces identical copies of) selected dsDNA molecules. Make 2 n copies (n : number of iteration) Solution filtering or amplification step!

(C) 2002, SNU Biointelligence Lab, PCR (Polymerase Chain Reaction)

(C) 2002, SNU Biointelligence Lab, Gel electrophoresis Molecular size fraction technique Detect the specific DNA Bead Separation Solution detection or filtering step!

48 Gel Electrophoresis

49 Complementary Magnetic Beads Magnet Bead Separation (1)

50 Bead Separation (2) Biotin (Vitamin H)

(C) 2002, SNU Biointelligence Lab, Restriction enzyme Cut the specific DNA site. Solution detection or filtering step! A A G C T T T T C G A A A T T C G A A C G T T A OH 3’ 3’ OH 5’ P P 5’ EcoRI