(C) 2002, SNU Biointelligence Lab, A Computer Scientist’s Guide to Molecular Biology...

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A Computer Scientist’s Guide to A Computer Scientist’s Guide to Molecular BiologyMolecular Biology

Biointelligence Lab.

Interdisciplinary Program in Cognitive Science,

Seoul National University

2002. 3. 20.

L. Kari et al., Soft Computing 5 (2001) 95-101

OutlineOutline

Introduction The DNA molecule The natural information contents of DNA

Transcription Editing Translation

Adleman’s in vitro experiment DNA as a computational tool

Biocomputing vs. BioinformaticsBiocomputing vs. Bioinformatics

MolecularMolecularBiologyBiology

ComputerComputerScienceScience

Bioinformatics

Molecular computingBiomolecular computingDNA computing

The DNA MoleculeThe DNA Molecule

DNA (DNA (ddeoxyriboeoxyribonnucleic ucleic aacid)cid) Schrödinger (1944): What is Life?

Our genes must essentialy be an aperiodic crystal Watson & Crick (1953): Nature 25: 737-738

Molecular Structure of Nucleic Acids: A structure for deoxyribose nucleic acid Nobel Prize, 1962.

DNA Structure (1) nucleotideDNA Structure (1) nucleotide

DNA Structure (2) ester bondDNA 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.

DNA Structure (3) base pairingDNA Structure (3) base pairing

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

DNA Structure (4) – double helixDNA Structure (4) – double helix

Watson-Crick complement

DNA Structure (5) – conformationDNA 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%).

The Natural Information Content of The Natural Information Content of DNADNA

Central DogmaCentral Dogma

Replicaton (1)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.

Replicaton (2)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

TranscriptionTranscription

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

EditingEditing

Capping

PolyAdenylation

RNA splicing

5’ Capping (1)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.

5’ Capping (2)5’ Capping (2) 3 functions of 5’ cap

protection of the RNA from degradation

translatability transport from the

nucleus to the cytoplasm

Polyadenylation (1)Polyadenylation (1)

Polyadenylation mechanism involves following steps:1. The cutting of the RNA chain at a particular site2. The addition of the poly [A] to the 3' end of the pre-mRNA3. The degradation of the remainder of the RNA transcript

Polyadenylation (2)Polyadenylation (2)

Two functions for

poly [A] on mRNA;

1. Protection

2. Translatability

RNA Splicing (1)RNA Splicing (1)

Translation (1)Translation (1)

tRNA structure

InitiationInitiation

Translation (5)Translation (5) ElongationElongation

Translation (6)Translation (6) TerminationTermination

The First DNA Computing The First DNA Computing MethodMethod

L. M. Adleman, Molecular Computation of Solutions to Combinatorial Problems,

Science, 266:1021-1024, 1994

First special DNA computerFirst 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.

Hamiltonian Path ProblemHamiltonian Path Problem

The Hamiltoian path problem: as the number of cities grows, even supercomputers have difficulty finding the path.

Adleman’s Molecular Computer: Adleman’s Molecular Computer: A Brute Force MethodA 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.

Encoding (Basic Concept)Encoding (Basic Concept)

AGCT TAGGP1A P1B

TAGG CATGP2A P2B

CGAT CGAAP3A P3B

P1B P3AP1B P2A

ATCC TACCATCC GCTA

ProcedureProcedureGenerate random paths

through the graph

Keep only those paths that begin with vin and end with vout

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 vin and vout

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 vi

AGCTTAGG

ATGGCATG

ATCCTACC

Vertex 1 Vertex 2

Edge 12

Step 1 : Hybridization

AGCTTAGG ATGGCATGATCC TACC

AGCTTAGGATCCTACC

Step 2 : Ligation

AGCTTAGGATGGCATGGAATCCGATGCATGGCTCGAATCC ACGTACCG

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

...... ...

ATGATG

ACGACG

TGCTGC

CGACGATAATAAGCAGCA

CGTCGT

......

Solution

PCR(Polymerase

Chain Reaction)

ATGTGCTAACGAACG

ACGCGAGCATAAATGTGCCGTACGCGAGCATAAATGTGCCGT

TAAACG

CGACGT

TAAACGGCAACG

CGACGTAGCCGT

ACGCGTAGCCGT

ACGCGT...

ACGGCATAAATGTGCACGCGT

ACGCGAGCATAAATGCGATGCCGT

......

.........

......

Decoding

LigationEncoding

Gel Electrophoresis

Affinity Column

ACGCGAGCATAAATGTGCACGCGT

ACGCGAGCATAAATGCGATGCACGCGT

ACGCGAGCATAAATGTGCACGCGT

ACGCGAGCATAAATGCGATGCACGCGT

Node 0 : ACG Node 3 : TAANode 1 : CGA Node 4 : ATGNode 2 : GCA Node 5 : TGC

Node 6 : CGT

DNA finds a solution!DNA finds a solution!

A Hamiltonian path with all vertices included is isolated and recovered

DNA as a Computational ToolDNA as a Computational Tool

DNA Memory 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

Complement Nucleotide

DNA bindingprocess

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

DNA MemoryDNA Memory

DNAmemory strands

a t c g g

t c a t ag c a c t

a t c g g

t c a t a

t a g c c c g t g a

Writing : make DNA sequences

Reading : hybridization and readout

DNA OperatorsDNA Operators

The bio-lab technology.

Hybridization Ligation Polymerase Chain Reaction (PCR) Gel electrophoresis Affinity separation (Bead) Enzymes: restriction enzyme…

Hybridization & LigationHybridization & 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!

DNA Hybridization & LigationDNA Hybridization & Ligation

CGTACCTTAGGCT

AGCTTAGGATGGCATGG AATCCGATGCATGGC

CGTACCTTAGGCTAGCTTAGGATGGCATGGAATCCGATGCATGGC

CGTACCTTAGGCT

AGCTTAGGATGGCATGGAATCCGATGCATGGC+

Ligation

Hybridization

Dehybridization

PCR (PCR (PPolymerase olymerase CChain hain RReaction)eaction)

Mullis: Nobel Prize (1993)

Amplifies (produces identical copies of) selected dsDNA molecules.

Make 2n copies (n : number of iteration)

Solution filtering or amplification step!

PCRPCR(Polymerase Chain Reaction)(Polymerase Chain Reaction)

Gel electrophoresisGel electrophoresis

Molecular size fraction technique

Detect the specific DNA

Bead SeparationBead Separation

Solution detection or filtering step!

Gel ElectrophoresisGel Electrophoresis

Complementary

Magnetic Beads

Magnet

Bead Separation Bead Separation (1)(1)

Bead Separation Bead Separation (2)(2)

Biotin (Vitamin H)

Restriction enzymeRestriction enzyme

Cut the specific DNA site. Solution detection or filtering step!

A A G C T T

T T C G A A

T T C G A

A C G T T

OH 3’

3’ OH

5’ P

P 5’EcoRI

(C) 2002, SNU Biointelligence Lab, A Computer Scientist’s Guide to Molecular Biology...

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