What makes DNA Computing
possible?
• Great advances in molecular biology
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PCR (Polymerase Chain Reaction)
DNA Selection by affinity
DNA Filtering
DNA Gel Electroforesis
DNA Denaturation Renaturation
DNA Restriction Enzymes
DNA Sequencing
• Ability to produce massive numbers of DNA
molecules with specified sequence and size
What is a typical methodology of
DNA Computing?
• Encoding: Map problem instance onto set
of biological molecules and molecular
biology protocols
• Molecular Operations: Let molecules react
to form potential solutions
• Extraction/Detection: Use protocols to
extract result in molecular form
What are the basics from
molecular biology that I need to
know to understand DNA
computing?
PHYSICAL STRUCTURE OF DNA
20 Å
5’ C
3’ OH
Minor Groove
34 Å
5’
3’
3’
5’
Sugar-Phosphate
Backbone
Major
Groove
Nitrogenous
Base
C 5’
3’ 0H
Central Axis
INTER-STRAND HYDROGEN BONDING
(+) (-)
(-) (+)
to Sugar-Phosphate
Backbone
Adenine
Thymine
to Sugar-Phosphate
Backbone
(-) (+)
(+) (-)
to Sugar-Phosphate
Backbone
(+) (-)
to Sugar-Phosphate
Backbone
Guanine
Hydrogen Bond
Cytosine
STRAND HYBRIDIZATION
Enzymes of Molecular Biology
•DNA Polymerase
•DNA Ligase, Helicase, Topoisomerase
•DNA Repair Ezymes
•DNA Recombinase
•Reverse Transcriptase
•Restriction Enzymes
•Nuclease
DNA Replication
• DNA is a double-helical molecule
• Each strand of the helix must be copied in
complementary fashion by DNA polymerase
• Each strand is a template for copying
• DNA polymerase requires template and primer
• Primer: an oligonucleotide that pairs with the end of
the template molecule to form dsDNA
• DNA polymerases add nucleotides in 5'-3' direction
DNA Polymerase
DNA Ligase


’
’


’
’
Ligase Joins 5' phosphate
to 3' hydroxyl
’
’
DNA Helicase
DNA Topoisomerase
DNA Damage Repair Enzymes
DNA Recombination Enzymes
Integrase
Reverse Transcriptase
Restriction Enzymes
• Bacteria have learned to "restrict" the
possibility of attack from foreign DNA by
means of "restriction enzymes"
• Type II and III restriction enzymes cleave
DNA chains at selected sites
• Enzymes may recognize 4, 6 or more bases in
selecting sites for cleavage
• An enzyme that recognizes a 6-base sequence
is a "six-cutter"
RESTRICTION ENDONUCLEASES
EcoRI
HindIII
AluI
HaeIII
Exo-Nuclease
Recombinant DNA Technology
•Cleavage DNA at specific sites by restriction enzymes,which greatly
facilitates the isolation and manipulation of individual DNA.
•Rapid sequencing of all the nucleotides in a purified DNA fragment,
which makes it possible to determine the boundaries of a gene and the
amino acid sequence it encodes.
• Nucleic acid hybridization, which makes it possible to find a specific
sequence of DNA or RNA.
•DNA cloning, whereby a single DNA molecule can be copied to
generate billions of identical molecules.
•DNA engineering, by which DNA sequences are altered to make
Modified versions of genes, which are reinserted back into cell.
RESTRICTION ENDONUCLEASES
EcoRI
HindIII
AluI
HaeIII
GEL ELECTROPHORESIS – Separation of DNA
fragments
Electrode
Samples
Slower
Gel
Buffer
Electrode
DNA molecules can be radioactively labeled
DNA Sequencing