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Transcript 
Biomolecule sizes
~3.4 nm
dsDNA
~1.8 nm
1/30/06
LaBean COMPSCI 296.5
Canons and Definitions



Biomolecules, biomacromolecules.
Structure determines Function.
Monomer, oligomer, polymer.


1/30/06
Deoxyribonucleotide, ribonucleotide, amino acid.
Configuration (covalent structure)
vs Conformation (3D structure).
LaBean COMPSCI 296.5
Central Dogma
DNA--> RNA--> Protein
1/30/06
LaBean COMPSCI 296.5
Biomolecules



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Lipids
Carbohydrates
Proteins
Nucleic acids
Goodsell
1/30/06
LaBean COMPSCI 296.5
ssDNA,
chemical
structure
Nucleoside (sugar + base)
Nucleotide (sugar + base + phosphate)
RAG & TYC
Purine (R ): adenine (A), guanine (G)
Pyrimidine (Y): thymine (T), cytosine (C )
1/30/06
LaBean COMPSCI 296.5
DNA structural details…
Propeller Twist. The bases of a DNA base pair are often
not precisely coplanar. They are twisted with respect to
each other, like the blades of a propeller.
1/30/06
LaBean COMPSCI 296.5
Complementary Base Pairing
5’ACCGGGTTTT 3’
3’TGGCCCAAAA 5’
aL=N
1/30/06
Annealing
Hybridization
5’ACCGGGTTTT 3’
..........
3’TGGCCCAAAA 5’
H-bond formation
Base pairing
45 = 1,024
410 = 1,048,576
4100 = 2 x1060
Number of sequences
of a given length
available.
LaBean COMPSCI 296.5
dsDNA, antiparallel helix
1/30/06
LaBean COMPSCI 296.5
DNA polymerization
1/30/06
LaBean COMPSCI 296.5
DNA replication
1/30/06
LaBean COMPSCI 296.5
Linear vs branched junctions
dsDNS
1/30/06
3-arm Junction
4-arm Junction
LaBean COMPSCI 296.5
DNA tiles
1/30/06
LaBean COMPSCI 296.5
Software and databases

Richardson Lab
 http://kinemage.biochem.duke.edu/



1/30/06
Molecular display and analysis software for all platforms (free!)
Nucleic acid database

http://ndbserver.rutgers.edu/

3D structure data for DNA and RNA
Protein Data Bank

http://www.rcsb.org/pdb/

3D structure data for proteins
LaBean COMPSCI 296.5
Why DNA in BioNano?

Programmable molecular recognition.


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Biotechnology infrastructure



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1/30/06
“smart velcro”
Understandable rules (WC base-pairing)
Large sequence space -- big library of addresses
Chemical synthesis of oligonucleotides
Enzymes for DNA manipulation and modification
Diverse attachment chemistry
Fairly stabile chemistry
LaBean COMPSCI 296.5
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