Biomedical Engineering Reference
In-Depth Information
solution-phase. synthesis. (for. cyclization. and. ligation. steps. that. proved. dificult. on. the.
solid.support).and.further.assembly.on.a.solid-phase.support.(Zhang.and.Seeman.1994)..
Each.reactive.species.contained.hairpin.sites.that,.upon.cleavage.by.a.restriction.enzyme,.
revealed.sticky.ends.that.could.be.hybridized.to.their.binding.partners.and.then.ligated.
to.form.a.stable.duplex.segment..The.solution-phase.ligations.had.yields.of.1%-10%.after.
puriication;. the. solid-phase. ligations,. when. they. went. at. all,. gave. yields. of. 30%-50%..
Similar.solid-phase.ligations.to.form.2D.polygons.had.earlier.been.shown.to.proceed.in.
nearly. quantitative. yield,. which. highlights. the. dificulty. of. processing. highly. branched.
DNA.with.native.ligation.enzymes..Since.seven.sequential.ligations.were.required.to.close.
the. sides. of. the. polyhedron,. the. overall. yield. of. product. was. small.. Characterization. of.
these.small.polyhedra.was.done.by.enzymatic.degradation.and.gel.electrophoresis;.and.
in.this.case,.the.closure.of.the.polyhedron.was.shown.to.proceed.“right.side.out.”.In.later.
work,. Turberield's. group. constructed. tetrahedral. structures. that. did. not. require. any.
ligation.steps;.these.DNA.nanostructures.assembled.in.high.yield.and.could.be.imaged.by.
AFM.(Goodman.et.al..2005,.2008,.Zhang.et.al..2010).
1.5 DNA Tiles and Tile Arrays
1.5.1 DNA Tiles
By.forming.double-crossover.DNA.tiles.with.complementary.sticky.ends,.Winfree.et.al..
(1998).made.repetitive.arrays.with.designed.stripes.of.periodicities.between.25.and.64.nm,.
where. the. observable. features. consisted. of. rows. of. DNA. hairpins. protruding. from. the.
surfaces. of. the. tiles. at. speciic. locations.. The. sizes. of. the. arrays. depended. on. careful.
control. of. oligo. stoichiometry. and. annealing. conditions;. crystals. up. to. 2.×.8.μm. were.
observed.. These. array. sizes. are. remarkable. because. no. ligation. step. was. involved;. the.
structure.is.entirely.held.together.by.noncovalent.interactions..The.arrays.could.be.labeled.
with.streptavidin/1.4.nm.nanogold.at.speciic.biotinylated.locations..All.the.imaging.was.
done. in. a. liquid. cell. under. isopropanol.. Later. work. showed. that. the. hairpin. loops. in.
tile.arrays.could.be.processed.by.ligation,.restriction,.or.further.annealing.to.change.the.
features. displayed. by. the. tiles. (Liu. et. al.. 1999).. It. was. also. found. to. be. feasible. to. pro-
duce.arrays.based.on.rhombus-shaped.tiles,.each.tile.containing.four.Holliday.junctions.
and. eight. different. oligonucleotides.. Each. rhombus. contained. eight. protruding. “sticky.
ends,”.which.were.designed.to.form.one-dimensional.(1D).or.2D.tile.arrays.after.thermal.
annealing;.the.assembly.was.done.in.one.step.from.oligonucleotides.by.slow.cooling.in.
a.water.bath.(Mao.et.al..1999)..Later.workers.focused.on.making.self-limiting.tile.arrays,.
usually. through. some. form. of. hierarchical. assembly.. Structures. up. to. 200.nm. in. size.
could.be.made,.although.these.nanostructures.often.suffered.from.poor.assembly.yields.
(Liu.et.al..2005,.Park.et.al..2006a)..Algorithmic.assembly.of.tiles.is.one.of.the.approaches.
used.in.computing.with.DNA;.a.beautiful.example.of.this.method.is.a.set.of.DNA.tiles.
that.self-assembles.into.Serpinski.triangle.(Rothemund.et.al..2004).
1.5.2 Making Tile Arrays
There.are.many.“recipes”.that.give.good.tile.arrays.(such.as.He.et.al..2005).and.due.to.the.
low.cost.of.the.DNA.oligos.required.for.this.type.of.DNA.nanostructure,.it.is.an.easy.entry.
point.into.the.ield.of.DNA.nanostructure.assembly..Assembly.and.imaging.of.high-quality.
