Biomedical Engineering Reference
In-Depth Information
In.another.productive.strategy.for.generation.of.3D.structures,.the.template.strand.of.the.
DNA.is.viewed.as.a.lexible.rod.that.can.be.coiled.and.“stitched”.to.itself.in.various.ways.
using.the.staple.strands..This.can.produce.3D.structures.in.which.the.DNA.helices.do.not.
all.lie.lat.on.a.surface.but.are.arranged.on.a.square.or.honeycomb.lattice.(Ke.et.al..2009a,.
Douglas.et.al..2009a,b)..This.design.strategy.can.also.produce.structures.like.a.rag.rug.or.
clay. coil.pot,.which. are. basically. 2D. surfaces. with. complex. curvature,. including. hollow.
spheres.and.bottle.shapes.(Dietz.et.al..2009,.Han.et.al..2011)..Extended.DNA.arrays.in.3D.
(DNA.crystals.with.designed.structures).were.the.original.motivation.for.Seeman's.studies.
on.DNA.nanostructures,.and.they.have.been.designed.and.made.with.crystal.structures.
that.can.be.solved.at.4.Å.resolution.(Zheng.et.al..2009).
1.6.4 reconfigurable DNA Nanostructures
Reconigurable.or.active.DNA.nanostructures.are.an.exciting.new.opportunity.in.nano-
science..A.straightforward.method.to.create.motion.is.the.use.of.segments.of.DNA.that.
can.switch.from.B-type.DNA.to.another.helical.conformation,.such.as.the.Z-helical.form,.
under. appropriate. ionic. conditions. (He. et. al.. 2007).. Of. course,. the. rest. of. the. structure.
must. be. made. of. sterner. stuff. that. can. retain. its. original. structure.. It. is. also. possible. to.
create.motion.by.cutting.a.critical.strand.of.DNA.enzymatically.or.by.using.strand.inva-
sion.to.replace.one.DNA.oligo.with.another..These.strategies.have.been.applied.in.DNA.
nanomachines.ranging.from.relatively.simple.DNA.“tweezers”.to.oligos.that.can.march.
along.a.piece.of.duplex.DNA.or.a.DNA.tile.track.(Yurke.et.al..2000,.Li.and.Tan.2002,.Tian.
et.al..2005),.to.a.DNA.“treadmill”.(Tian.and.Mao.2004).to.more.elaborate.tile.assemblies.
with. portions. that. rotate. around. a. hinge. region. (Yan. et. al.. 2002,. Feng. et. al.. 2003,. Ding.
and. Seeman. 2006).. In. one. such. “machine,”. rotatable. cassettes. were. inserted. into. DNA.
origami.templates.and.used.to.capture.various.target.DNA.tiles.(Gu.et.al..2009)..In.this.
latter.case,.thermal.annealing.was.used.for.error.correction.after.addition.of.each.tile..By.
carefully.controlling.the.assembly.conditions.between.37°C.and.40°C,.a.high.yield.of.cor-
rect.assembly.was.obtained..Other.DNA.nanostructures.have.been.designed.as.tracks.for.
DNA-based.“walkers.”.These.hairpin.structures.move.from.one.target.strand.to.another.
through.selective.hybridization,.often.fueled.by.consumption.of.a.“fuel”.strand.that.can.
provide.energy.for.unidirectional.motion..It.was.a.natural.step.to.place.the.target.strands.
upon. a. DNA. origami. framework. containing. cargos. loaded. into. rotatable. cassettes;.
a. “walker”. was. able. to. travel. along. the. origami. and. pick. up. cargo. from. the. cassettes.
(Gu.et.al..2010)..By.programming.the.cassettes,.the.cargo.could.be.whisked.into.an.inac-
cessible.position.to.the.walker.
Mechanical.motion.can.also.be.created.by.release.of.a.latch,.as.in.the.lid.of.the.DNA.
box.shown.in.Figure.1.8..As.shown.in.panel.a,.the.lid.is.initially.held.closed.by.two.short.
duplex.DNA.“latches.”.Each.latch.includes.a.toehold.segment,.so.it.can.be.unlocked.by.a.
complementary.oligonucleotide.via.strand.invasion..Addition.of.the.two.complementary.
oligos.unlocks.both.latches,.releasing.the.lid..Opening.of.the.lid.can.be.monitored.either.
by.AFM.of.individual.boxes,.or.in.bulk.solution,.by.luorescence.resonance.energy.trans-
fer.(FRET).between.a.donor.and.a.acceptor.dye.incorporated.into.staple.strands.on.the.
rim.of.the.box.and.on.the.lid.of.the.box.(Andersen.et.al..2009)..A.recent.report.describes.
the.use.of.a.“clamshell”.illed.with.bioactive.proteins,.where.the.“shell”.is.held.closed.
by.DNA.aptamers..The.aptamers.recognize.and.bind.to.speciic.cell.types,.causing.the.
clamshell.to.open.and.releasing.proteins.that.initiate.programmed.cell.death.(Douglas.
et.al..2012)..The.use.of.strand.invasion.for.reconiguration.of.a.DNA.origami.was.brought.
to.the.nth.degree.in.a.case.study.of.a.DNA.Möbius.strip,.shown.in.Figure.1.8—strand.
