DNA nanotechnology

What is DNA nanotechnology?

 * Structural DNA nanotechnology involves the construction of inflexible objects out of DNA. The DNA itself provides both the rigidity and the connectivity of the objects. Thus DNA serves as both brick and mortar. To achieve rigidity and complex connectivity, paranemic crossover (PX) and/or antiparallel double crossover (DX) motifs generally are employed.


 * Compositional DNA nanotechnology involves the use of DNA as mortar only, and the DNA generally does not provide structural integrity. The distinction between structural and compositional DNA nanotechnology was made by Ned Seeman, the founder of the field (Seeman NC, At the Crossroads of Chemistry, Biology, and Materials: Structural DNA Nanotechnology, Chemistry and Biology 10, 1151–1159, 2003.)


 * Other types of DNA nanotechnology include DNA computers, DNA aptamers, and DNAzymes. It is natural to consider the larger field of nucleic acid nanotechnology in order to include structures and devices made of RNA or DNA/RNA hybrids. The boundaries of the field are further blurred when considering related synthetic materials such as PNA (so-called peptide nucleic acid). DNA objects that can be copied by polymerases are examples of clonable DNA nanotechnology.

What makes DNA good for building small?

 * DNA can be exploited for programmable self-assembly of well-defined, chemically anisotropic structures.
 * DNA features association governed by sequence complementarity.
 * Double-stranded DNA is rigid, structurally regular, and addressable (through sequence-specific recognition).


 * DNA can be cloned and replicated through template-directed enzymatic polymerization.
 * DNA replication is made feasible thanks to sequence complementarity and to DNA polymerases.
 * DNA replication facilitates the exponential amplification of chemically homogenous objects.
 * DNA replication facilitates the directed molecular evolution of novel DNA devices.
 * DNA replication facilitates the self-assembly of long, information-rich templates.


 * Powerful enzymatic tools are available for sequence-specific manipulation.
 * Short single strands of DNA of arbitrary sequence are easy to chemically synthesize.

What categories of tools can be made with DNA nanotechnology?
Tools for biophysics
 * Tools for observing and perturbing structure and energetics (kinetics and thermodynamics)
 * Conformational changes
 * Association/disassociation
 * Catalysis
 * Tools for building model systems
 * "What I cannot create, I cannot understand." --Richard Feynman
 * "The Third Culture" --Kevin Kelly ref

Tools for cell biology
 * Tools for observing and perturbing cellular behavior
 * Improvement to spectroscopic tools (quantum dot probes, force spectroscopy)
 * Complex readout of cellular state

Tools for medicine
 * Translation and readout for combinatorial drug libraries
 * Medical imaging
 * Caged gadolinium for MRI gated by mRNA expression levels
 * Replacement of defective cellular components
 * Molecular motors, pumps, etc. for delivering molecules within a cell
 * Molecular scavengers for early diagnosis
 * Drug delivery with superior targeting and barrier avoidance

Tools for chemistry
 * Algorithmic assembly
 * Better affinity reagents for detection or purification
 * Biosensors
 * DNA sequencing tools
 * Tools for detecting polymorphisms
 * Protective coatings
 * Polymers
 * Catalysts (e.g. scaffold enhanced)
 * Filters
 * Batteries, fuel cells

Tools for building molecular computers
 * High-density molecular memory arrays
 * Quantum computers

Tools for material synthesis
 * Translation and readout for other combinatorial libraries
 * Nanoscale transport

What are general strategies for attaching proteins to DNA scaffolds?

 * Rigid attachment of proteins is important for molecular imaging applications and for hybrid DNA-protein machines
 * In some cases, multiple attachments between the protein and DNA may increase the rigidity of the complex
 * Example with 3+ attachments
 * Intein-mediated ligation of oligonucleotide-cysteine to the N-terminus of the protein plus
 * tandem zinc-finger binding domains fused to the C-terminus of the protein plus
 * non-specific lysine coupling at a third locus


 * Non-site-specific attachment of oligonucleotide to protein
 * Usually through covalent conjugation; check out http://www.probes.com/
 * Reaction with lysines
 * Amine attacking n-hydroxysuccinimide (NHS) ester
 * Reaction with cysteines
 * Thiol attacking maleimide
 * Disulfide exchange
 * Thiol attachment to gold
 * Reaction with aspartates and glutamates
 * Carboxylate activation with EDC/NHS, followed by attack with amines
 * Reaction with serines, threonines, and tyrosines?
 * Reaction with arginines?
 * We are more interested in site-specific attachment of proteins to DNA scaffolds


 * Site-specific
 * Not requiring genetic modification of protein
 * Antibodies
 * Aptamers
 * Requiring genetic modification of protein
 * Fusion to DNA-binding motifs
 * Tandem zinc finger motifs
 * Expressed protein ligation to oligonucleotide

How can DNA scaffolds be made to interface with the macroscopic world?

 * We are interested in parallel interfacing with many DNA objects as well as in specific addressing of individual DNA objects within a population.
 * Light
 * Sound?
 * Heat
 * Pressure change
 * pH change
 * Radio waves
 * Manual addition of reagents
 * Voltage change

Links

 * Ned Seeman
 * Eric Winfree
 * Paul Rothemund
 * William Shih
 * Hao Yan
 * Chengde Mao
 * John Reif
 * Andrew Turberfield
 * Milan Stojanovic
 * Nucleic acid nomenclature and structure