What makes DNA Computing possible?
33
What makes DNA Computing possible? • Great advances in molecular biology – 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
description
What makes DNA Computing possible?. Great advances in molecular biology PCR (Polymerase Chain Reaction) DNA Selection by affinity DNA Filtering DNA Gel Electroforesis DNA Denaturation Renaturation DNA Restriction Enzymes DNA Sequencing - PowerPoint PPT Presentation
Transcript of What makes DNA Computing possible?
What makes DNA Computing possible?
• Great advances in molecular biology– 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
• 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 is a typical methodology of DNA Computing?
What are the basics from molecular biology that I need to
know to understand DNA computing?
PHYSICAL STRUCTURE OF DNA
20 Å
Nitrogenous Base
34 Å
MajorGroove
Minor Groove
Central Axis
Sugar-PhosphateBackbone
5’ C3’ OH
3’ 0HC 5’
5’
3’
3’
5’
INTER-STRAND HYDROGEN BONDING
Adenine Thymine
to Sugar-PhosphateBackbone
to Sugar-PhosphateBackbone
(+) (-)
(+)(-)
Hydrogen Bond
Guanine Cytosine
to Sugar-PhosphateBackbone
to Sugar-PhosphateBackbone
(-) (+)
(+)(-)
(+)(-)
STRAND HYBRIDIZATION
Enzymes of Molecular Biology•DNA Polymerase•DNA Ligase, Helicase, Topoisomerase•DNA Repair Ezymes•DNA Recombinase•Reverse Transcriptase•Restriction Enzymes•Nuclease
• 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 Replication
DNA Polymerase
DNA Ligase
’ ’
’ ’
Ligase Joins 5' phosphateto 3' hydroxyl
’ ’
DNA Helicase
DNA Topoisomerase
DNA Damage Repair Enzymes
DNA Recombination Enzymes
Integrase
Reverse Transcriptase
• 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 Enzymes
RESTRICTION ENDONUCLEASES
EcoRI
HindIII
AluI
HaeIII
- OH 3’
5’ P -
- P 5’
3’ OH -
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 theamino 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
- OH 3’
5’ P -
- P 5’
3’ OH -
BufferGel
Electrode
Electrode
Samples
Faster
Slower
GEL ELECTROPHORESIS – Separation of DNA fragments
DNA molecules can be radioactively labeled
DNA Sequencing
