Biomedical Engineering Reference
In-Depth Information
Figure 1.3
(See companion CD for color igure.)
.Crossover.junction.schematic,.cartoon.drawn.using.PDB.sequence.1NVN,.
green.dots.=.Ca
2+
.ions..(Crystal.data.from.Cardin,.C.J..et.al.,.Structural.analysis.of.two.Holliday.junctions.formed.
by.the.sequences.TCGGTACCGA.and.CCGGTACCGG,.DOI:.10.2210/pdb1nvn/pdb,.http://www.rcsb.org/pdb/
explore.do?structureId=1NVN,.accessed.July.23,.2012.)
good. behavior. and. tended. to. aggregate.. This. paper. also. probed. several. isomerization.
processes. seen. in. double. crossover. structures.. Branch. migration. can. occur. if. the. DNA.
sequence.permits.simultaneous.adjustment.of.the.locations.of.both.crossover.sites;.if.only.
one. crossover. can. migrate,. a. torsional. strain. will. be. created. in. the. DNA. tile.. Crossover.
isomerization.interchanges.the.positions.of.the.helical.and.crossover.(bent).oligos;.it.is.facile.
in.single.crossover.structures,.but.does.not.occur.in.tiles.in.which.multiple.crossover.sites.
lie.within.a.few.turns.of.the.DNA.helix..Thus,.by.placing.two.or.more.crossovers.between.
two.DNA.helices,.stable.nanostructures.with.well-deined.shapes.could.be.created.
1.4.2 3D Nanostructures Based on Holliday Junctions
Chen. and. Seeman. (1991). constructed. the. irst. rationally. designed. DNA. polyhedron.
structure:.a.cube.built.from.10.synthetic.DNA.oligonucleotides..The.cube.contained.several.
catenated.loops.of.DNA,.whose.assembly.required.several.intermediate.ligation.and.gel-
electrophoretic. puriication. steps.. The. typical. yield. from. the. ligation. steps. was. about.
10%.per.reaction..The.purity.of.the.cube.product.was.determined.by.gel.electrophoresis.
and. its. topology. by. analysis. of. the. cleavage. products. at. speciic. restriction. sites. in. the.
different. cube. edges.. Although. it. was. not. possible. to. determine. whether. the. cube. was.
constructed. “right. side. out”. or. “inside. out,”. this. paper. showed. that. by. combining.
crossover.junctions.and.“sticky.ends,”.DNA.could.be.used.like.a.Tinkertoy.to.construct.
arbitrary.nanostructures..In.order.to.overcome.some.of.the.yield.limitations.of.the.solution-
phase.synthesis.of.the.DNA.cube,.a.truncated.octahedron.was.built.by.a.combination.of.
