(c) 2002, snu biointelligence lab, a computer scientist’s guide to molecular biology...
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(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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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
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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OutlineOutline
Introduction The DNA molecule The natural information contents of DNA
Transcription Editing Translation
Adleman’s in vitro experiment DNA as a computational tool
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Biocomputing vs. BioinformaticsBiocomputing vs. Bioinformatics
MolecularMolecularBiologyBiology
ComputerComputerScienceScience
Bioinformatics
Molecular computingBiomolecular computingDNA computing
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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The DNA MoleculeThe DNA Molecule
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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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.
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DNA Structure (1) nucleotideDNA Structure (1) nucleotide
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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.
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DNA Structure (3) base pairingDNA Structure (3) base pairing
Complimentary base pairing accounts for the Chargaff’s rule (A=T, G=C).
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DNA Structure (4) – double helixDNA Structure (4) – double helix
Watson-Crick complement
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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%).
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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The Natural Information Content of The Natural Information Content of DNADNA
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Central DogmaCentral Dogma
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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.
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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
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TranscriptionTranscription
Scientists snap first 3-D pictures of the "heart" of the transcription machine.
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EditingEditing
Capping
PolyAdenylation
RNA splicing
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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.
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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
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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
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Polyadenylation (2)Polyadenylation (2)
Two functions for
poly [A] on mRNA;
1. Protection
2. Translatability
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RNA Splicing (1)RNA Splicing (1)
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RNA Splicing (2)RNA Splicing (2)
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RNA Splicing (3)RNA Splicing (3)
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Translation (1)Translation (1)
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Translation (2)Translation (2)
tRNA structure
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Translation (3)Translation (3)
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Translation (4)Translation (4)
InitiationInitiation
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Translation (5)Translation (5) ElongationElongation
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Translation (6)Translation (6) TerminationTermination
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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The First DNA Computing The First DNA Computing MethodMethod
L. M. Adleman, Molecular Computation of Solutions to Combinatorial Problems,
Science, 266:1021-1024, 1994
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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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.
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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Hamiltonian Path ProblemHamiltonian Path Problem
The Hamiltoian path problem: as the number of cities grows, even supercomputers have difficulty finding the path.
1
0
3
2 5
6
4
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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.
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Encoding (Basic Concept)Encoding (Basic Concept)
1
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AGCT TAGGP1A P1B
TAGG CATGP2A P2B
CGAT CGAAP3A P3B
P1B P3AP1B P2A
10
3
2 56
4
ATCC TACCATCC GCTA
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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
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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
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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HPP
...
...... ...
ATGATG
ACGACG
TGCTGC
CGACGATAATAAGCAGCA
CGTCGT
......
...
...
......
......
10
3
2 5
6
4
Solution
PCR(Polymerase
Chain Reaction)
ATGTGCTAACGAACG
ACGCGAGCATAAATGTGCCGTACGCGAGCATAAATGTGCCGT
TAAACG
CGACGT
TAAACGGCAACG
...
...
...
...
CGACGTAGCCGT
...
...
...
ACGCGAGCATAAATGTGCCGTACGCGAGCATAAATGTGCCGT
ACGCGTAGCCGT
ACGCGT...
...
...
...
...
ACGGCATAAATGTGCACGCGT
ACGCGAGCATAAATGCGATGCCGT
ACGCGAGCATAAATGTGCCGTACGCGAGCATAAATGTGCCGT
......
.........
ACGCGAGCATAAATGTGCCGTACGCGAGCATAAATGTGCCGT
...
......
...
...
Decoding
LigationEncoding
Gel Electrophoresis
Affinity Column
ACGCGAGCATAAATGTGCACGCGT
ACGCGAGCATAAATGCGATGCACGCGT
ACGCGAGCATAAATGTGCACGCGT
ACGCGAGCATAAATGCGATGCACGCGT
2
01
3 4
5
6
Node 0 : ACG Node 3 : TAANode 1 : CGA Node 4 : ATGNode 2 : GCA Node 5 : TGC
Node 6 : CGT
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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DNA finds a solution!DNA finds a solution!
A Hamiltonian path with all vertices included is isolated and recovered
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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DNA as a Computational ToolDNA as a Computational Tool
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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
A
C
T
G
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
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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DNA MemoryDNA Memory
DNAmemory strands
a t c g g
t c a t ag c a c t
0 0 0
a t c g g
t c a t a
1 0 1
t a g c c c g t g a
Writing : make DNA sequences
Reading : hybridization and readout
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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DNA OperatorsDNA Operators
The bio-lab technology.
Hybridization Ligation Polymerase Chain Reaction (PCR) Gel electrophoresis Affinity separation (Bead) Enzymes: restriction enzyme…
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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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!
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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DNA Hybridization & LigationDNA Hybridization & Ligation
CGTACCTTAGGCT
AGCTTAGGATGGCATGG AATCCGATGCATGGC
CGTACCTTAGGCTAGCTTAGGATGGCATGGAATCCGATGCATGGC
CGTACCTTAGGCTAGCTTAGGATGGCATGGAATCCGATGCATGGC
CGTACCTTAGGCT
AGCTTAGGATGGCATGGAATCCGATGCATGGC+
+
Ligation
Hybridization
Dehybridization
(C) 2002, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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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!
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PCRPCR(Polymerase Chain Reaction)(Polymerase Chain Reaction)
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Gel electrophoresisGel electrophoresis
Molecular size fraction technique
Detect the specific DNA
Bead SeparationBead Separation
Solution detection or filtering step!
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Gel ElectrophoresisGel Electrophoresis
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Complementary
Magnetic Beads
Magnet
Bead Separation Bead Separation (1)(1)
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Bead Separation Bead Separation (2)(2)
Biotin (Vitamin H)
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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
A
T T C G A
A C G T T
A
OH 3’
3’ OH
5’ P
P 5’EcoRI