Biomedical Engineering Reference
In-Depth Information
nanostructures..Cryo-electron.microscopy.results.for.large.3D.DNA.nanostructures.also.
show.bulged.or.twisted.structures.
DNA. is. extremely. sturdy. as. far. as. biomolecules. are. concerned,. but. it. must. be. han-
dled. with. care. in. order. to. perform. as. a. structural. material.. Unlike. most. engineering.
materials,.DNA.oligos.are.edible.and.must.be.protected.from.adventitious.bacteria.and.
enzymes..Duplex.DNA.requires.water,.controlled.pH,.and.controlled.concentrations.of.
mono-.and.divalent.cations.to.assemble..While.DNA.nanostructures.can.be.kinetically.
trapped. after. assembly. by. drying. or. solvent. exchange,. the. long-term. stability. of. such.
structures.has.not.been.established..Although.there.are.many.proposals.for.use.of.DNA.
nanostructures.as.delivery.devices.or.diagnostic.markers.for.use.in.living.organisms,.it.
is.not.clear.how.well.such.nanostructures.survive.in.different.biological.systems,.how.
they. partition. in. cells. or. organisms,. or. whether. they. can. excite. an. immune. response..
DNA.nanostructures,.particularly.3D.ones,.are.slow.to.assemble,.and.assembly.yields.
for.large.or.3D.structures.are.generally.poor..Although.most.DNA.nanostructures.are.
primarily.characterized.by.AFM,.surface.attachment.is.still.poorly.understood.and.con-
trolled..Finally,.from.a.standpoint.of.creation.of.functional.devices.and.materials,.nor-
mal.DNA.is.not.very.interesting.electronically,.optically,.or.magnetically..Of.course,.all.
these. limitations. are. also. opportunities. for. researchers. who. want. to. enter. the. ield. of.
DNA.nanostructures.
1.3 DNA Oligonucleotides and Duplex DNA
Single-stranded.(ss).DNA.is.the.raw.material.used.for.construction.of.DNA.nanostructures..
It. consists. of. DNA. bases. attached. to. 2-deoxyribose. sugar. units;. these. units. are. linked.
together. through. phosphodiester. bonds. between. the. 3′. and. 5′. carbons. on. neighboring.
sugars..Thus,.oligonucleotides.have.a.3′.end.and.a.5′.end..In.duplex.DNA.(Figure.1.1),.the.
strand. directions. run. antiparallel—that. is,. the. 3′. end. of. one. oligonucleotide. lies. next. to.
the.5′.end.of.the.complementary.oligonucleotide..The.oligonucleotides.are.held.together.
by.a.combination.of.hydrogen.bonding.between.the.complementary.DNA.bases.and.base-
stacking.interactions.that.help.to.hide.the.hydrophobic.DNA.bases.from.exposure.to.water..
In.normal.B-form.DNA,.the.helix.repeat.length.is.10.4.bases,.which.corresponds.to.about.
3.5.nm. per. turn. of. the. helix.. Thus,. a. duplex. segment. 70.nm. in. length. would. require. 20.
turns.of.the.duplex.or.208.base.pairs..Getting.this.DNA.presents.a.practical.problem,.for.if.
the.oligos.are.constructed.synthetically,.the.longer.the.sequence,.the.worse.the.yield.
1.3.1 Short Oligos: Sources and Handling
Most.DNA.nanostructures.rely.on.short.oligonucleotides.(<80.bp).that.can.easily.be.made.
by.solid-phase.synthesis..Many.companies.can.produce.custom.sequences.with.a.1-3.day.
turnaround. at. synthesis. scales. ranging. from. nanomolar. to. millimolar. and. with. many.
options. for. synthetic. modiication. of. the. nucleotides.. Puriication. by. high-performance.
liquid.chromatography.is.recommended.for.oligos.above.about.50.bp.in.length,.or.those.
that. contain. synthetic. modiications,. such. as. luorophores. or. thiol. groups,. and. is. also.
recommended.for.oligos.that.are.to.be.used.to.make.stoichiometric.structures.such.as.tile.
arrays..Oligonucleotides.can.also.be.purchased.as.crude.desalted.and.lyophilized.solids.
in. a. 96-well. plate. or. as. solutions. of. such. material. made. up. to. a. speciic. optical. density.
