Biomedical Engineering Reference
In-Depth Information
substrates..However,.almost.all.AFM.studies.of.origami.use.mica.as.the.substrate,.because.
DNA.nanostructures.bind.poorly.to.anionic.silicon.dioxide.under.most.deposition.condi-
tions.. This. is. because. DNA. is. a. polyanion. with. high. charge. density.. Mica. is. an. anionic.
surface,.but.it.has.a.high.afinity.for.Mg
2+
.ion,.which.is.present.in.most.DNA.annealing.
buffers.at.∼10.mM..Mg
2+
.adheres.to.the.mica.surface.at.sites.usually.occupied.by.monova-
lent.ions.like.sodium.or.potassium,.causing.a.partial.charge.reversal.that.allows.DNA.to.
stick.to.the.surface.
Charge.reversal.does.not.work.as.well.on.native.silicon.oxide.because.the.anionic.charge.
density.of.this.surface.is.much.lower.than.that.of.mica..However,.by.treating.the.silicon.
surface. with. oxygen. plasma,. a. more. highly. charged. oxide. is. formed. that,. in. the. pres-
ence.of.somewhat.higher.magnesium.concentrations.(∼100.mM),.can.bind.DNA.origami.
strongly.enough.for.good.imaging.under.luid..By.using.a.lithographic.mask.to.pattern.
the. plasma-etched. oxide. regions,. it. is. possible. to. direct. the. binding. and. orientation. of.
individual.DNA.origami.on.substrates.such.as.diamond-like.carbon.and.silicon.(Kershner.
et.al..2009,.Hung.et.al..2010)..This.was.an.important.inding.because.it.showed.that.the.
DNA.origami.could.act.as.an.intermediary.between.lithography.(done.at.30-60.nm.reso-
lutions). and. sub-10.nm. patterning. (done. by. placing. metal. nanoparticles. onto. the. DNA.
origami.in.programmed.locations)..By.replacing.the.deposition.buffer.with.successively.
higher.concentrations.of.ethanol,.the.surface.containing.the.patterned.DNA.origami.and.
their. attached. nanoparticles. could. be. removed. from. the. liquid. and. dried. for. imaging.
in. air.. As. an. alternative. approach. to. the. use. of. magnesium. cations. for. charge. reversal,.
cationic.self-assembled.monolayers.(SAMs).can.be.deposited.on.silicon.dioxide.via.silox-
ane.chemistry..These.SAMs.provide.robustly.attached.surface.charges.that.anchor.DNA.
nanostructures.and.origami,.and.the.SAM-anchoring.layers.can.also.be.lithographically.
patterned.to.direct.the.binding.of.individual.DNA.origami.or.tile.assemblies.on.silicon.
(Gao.et.al..2010,.Sarveswaran.et.al..2010,.Penzo.et.al..2011)..The.DNA.origami.deposited.
on. these. cationic. SAMs. are. persistently. attached. to. the. silicon. oxide. and. can. be. rinsed.
with.buffer.or.water.before.imaging.in.air..A.critical.requirement.for.successful.visual-
ization.of.DNA.origami.on.oxide.surfaces.is.low.surface.roughness.(below.about.0.5.nm.
root-mean-square).. Clean. native. oxide. surfaces. easily. meet. this. roughness. metric,. but.
thicker. oxides. or. glass. surfaces. can. be. more. troublesome.. A. recent. study. showed. that.
very.smooth.oxide.surfaces.suitable.for.binding.and.imaging.of.DNA.origami.could.be.
attained. with. hydrogen. silsesquioxane. (HSQ).. HSQ. is. a. spin-on. glass. coating. material,.
which.offers.the.possibility.of.overcoating.other.substrates.or.even.performing.multilevel.
patterning.of.DNA.nanostructures.(Shah.et.al..2012).
There. are. several. other. substrates. that. have. been. used. successfully. with. DNA.
nanostructures..Just.as.thiols.can.be.used.to.attach.gold.nanoparticles.to.DNA.origami,.
several. groups. have. used. the. strong. interactions. between. thiols. and. gold. to. anchor.
DNA. nanostructures. to. surfaces. in. desired. locations.. Speciic. staple. strands. that.
are. synthetically. modiied. with. thiol. groups. are. inserted. into. DNA. nanostructures,.
and. these. thiols. stretch. the. DNA. nanostructures. between. appropriately. spaced. gold.
posts.or.gold.pads.on.a.surface.that.is.otherwise.repulsive.(Ding.et.al..2010b,.Pearson.
et. al.. 2011).. Graphene. is. an. attractive. substrate. for. electronic. and. electromechanical.
applications;.recent.work.shows.that.DNA.origami.adhere.well.to.both.graphene.oxide.
and.to.graphene.oxide.after.reduction.in.a.nitrogen/hydrogen.mixture..The.graphene.
can. be. patterned. effectively. by. irst. depositing. graphene. oxide. lakes. onto. a. cationic.
SAM. on. silicon,. next. lithographically. patterning. and. plasma. etching. the. graphene.
oxide,.and.inally,.removing.the.resist.and.reducing.the.graphene.oxide.(Yun.et.al..2012).
