Biomedical Engineering Reference
In-Depth Information
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Figure 1.5
(See companion CD for color igure.)
. Use. of. Cadnano. for. design. of. 3D. DNA. origami. blocks.. Screenshot.
(a).shows.user.interface,.(b).shows.helix.map.with.scaffold.strand.and.program-generated.staple.strands,.(c-e).
show. steps. along. the. design. process,. and. (f). is. the. rendered. 3D. structure.. (Reprinted. with. permission. from.
Douglas,.S.M..et.al.,.
Nucl. Acids Res
.,.37,.5001,.2009b.under.terms.of.open.source.agreement.)
a. self-assembling. tetrahedral. nanostructure. about. 50.nm. in. size,. with. an. interior. cavity.
large.enough.to.contain.most.types.of.virus.capsids..The.tetrahedra.were.self-assembled.by.
thermally.annealing.an.M13.mp18.template.strand.with.the.staple.mix.of.248.short.oligos..
AFM.imaging.was.not.satisfactory.due.to.the.tip.squashing.the.3D.objects.down.to.a.total.
height.of.4-5.nm,.but.high-resolution.transmission.electron.microscopy.(TEM).of.tetrahedra.
stained.with.uranyl.formate.showed.about.a.40%.yield.of.correctly.formed.nanostructures..
Interestingly,.the.vertices.of.the.tetrahedra,.which.consisted.of.unstructured.regions.of.the.
DNA.template.strand,.appear.as.distinct.light.features.in.the.high-resolution.TEM.images..
The.folded.structures.were.further.characterized.in.solution.by.dynamic.light.scattering.at.
a.2.nM.concentration;.and.the.measured.hydrodynamic.radius.(20.7.±.1.nm).was.close.to.the.
theoretical.expectation.(24.6.nm)..It.is.possible.for.such.a.tetrahedral.structure.to.fold.up.with.
different.faces.of.the.lat.DNA.origami.presented.to.the.outside.world,.and.the.distribution.
of.these.two.isomers.in.the.folded.tetrahedra.was.not.determined.
Another.approach.for.construction.of.3D.objects.is.to.view.the.DNA.as.a.set.of.rods.and.
strings..Duplex.DNA.has.a.persistence.length.of.about.50.nm,.but.bundles.of.helices.are.
much.more.rigid.(Mathieu.et.al..2005)..An.early.demonstration.of.folding.of.DNA.directed.
by.a.template.strand.used.sets.of.helix-bundle.rods.held.together.by.lexible.connections.
to. form. an. octahedron.. The. structure. used. a. 1669.bp. heavy. chain,. constructed. by. solid-
phase. synthesis. and. PCR. assembly,. then. cloned. into.
E. coli
. for. production,. and. assisted.
