Biomedical Engineering Reference
In-Depth Information
tile.arrays.requires.some.trial.and.error..The.size.of.the.growing.array.is.determined.by.
several. factors,. including. the. annealing. rate. and. the. limiting. oligo. concentration.. The.
concentrations.of.the.individual.oligos.should.be.assayed.by.UV-Vis.to.enable.optimization.
of.the.stoichiometric.ratios.of.the.oligos..Annealing.from.95°C.to.room.temperature.over.
24-48.h. is. necessary. for. assembly. of. micron. scale. structures.. The. tile. arrays. are. fragile;.
sonication,. vigorous. mixing,. and. iltration. to. dryness. will. tear,. fold,. or. degrade. them..
Finally,.good.AFM.images.may.require.trying.multiple.tips.and.imaging.conditions.
1.5.3 Assembly of Tile Arrays in Presence of the Substrate
Interactions. between. DNA. nanostructures. and. surfaces. can. be. drawn. upon. to. facilitate.
large.scale.self-assembly.of.tile.arrays.with.low.defect.density.(Hamada.and.Murata.2009,.
Sun. et. al.. 2009).. For. example,. a. 2D. DNA. tile. array. requiring. only. three. oligonucleotide.
components.was.pre-annealed.from.95°C.to.60°C.in.solution,.at.which.point.tiles.are.pres-
ent.but.unable. to.assemble. into.arrays,. and.then.incubated. on.mica. surfaces.at.50°C.for.
16.h..The.intertile.interaction.at.50°C.was.not.large.enough.to.allow.formation.of.2D.arrays.
in.solution.because.the.“sticky.ends”.involved.were.only.4-6.bases.long,.but.in.the.pres-
ence.of.the.mica.surface,.the.tiles.formed.a.nearly.continuous.2D.array.over.the.mica..This.
is. an. exciting. result. because. it. suggests. that. by. careful. surface. modiication,. it. may. be.
feasible.to.direct.the.growth.of.DNA.arrays.to.speciic.locations.
1.5.4 Decoration of Tile Arrays
There. are. now. many. examples. of. the. use. of. DNA. tile. arrays. to. template. assembly. of.
non-DNA. components.. For. example,. 21. oligonucleotides. were. assembled. into. a. 2D. tile.
array.that.included.a.periodically.placed.ss.hybridization.site.(poly-A)..Addition.of.gold.
nanoparticles.functionalized.with.DNA.oligonucleotides.(poly-T).formed.regular.rows.of.
the.nanoparticles,.but.since.the.hybridization.sites.were.4.nm.apart.and.the.nanoparticles.
had.a.6.nm.diameter,.many.sites.did.not.capture.a.nanoparticle.(Le.et.al..2004)..A.similar.
result.(sparse.spacing.of.DNA-functionalized.nanoparticles).was.observed.by.Zhang.et.al..
(2006). for. binding. sites. constructed. on. the. surface. of. a. DNA. grid. and. was. attributed. to.
electrostatic.repulsion.between.the.multiple.oligos.coating.the.nanoparticles..2D.arrays.of.
DNA.have.been.used.to.grab.proteins.in.speciic.orientations.for.cryo-electron.microscopy.
studies.(Selmi.et.al..2011).
1.6 DNA Origami
1.6.1 Overview
In. the. DNA. origami. technique. (Yan. et. al.. 2003a,. Rothemund. 2005,. 2006),. a. long,. single.
strand.of.DNA,.called.the.template.strand,.is.folded.into.a.desired.2D.or.3D.shape..Folding.
is. induced. by. base-pairing. interactions. between. the. template. strand. and. hundreds. of.
short.synthetic.oligonucleotides.or.“staple.strands.”.Amazingly,.these.hundreds.of.discrete.
folding.interactions.take.place.simultaneously.during.annealing,.resulting.in.high.yields.
(up. to. 90%. or. 95%). of. properly. folded. DNA. origami.. Design. principles. are. suficiently.
understood.that.DNA.nanostructures.with.novel,.arbitrary.shapes.can.move.from.concept.
to.reality.in.about.2.weeks.
