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