Biomedical Engineering Reference
In-Depth Information
RNA. also. forms. an. essential. component. of. RNA/protein. complexes,. which. form.
spliceosomes. and. ribosomes. (Czernilofsky. et. al.. 1974;. Berget. et. al.. 1977;. Chow. et. al..
1977).. Unfortunately,. noncanonical. pairings. are. very. dificult. to. predict. with. only. the.
RNA.sequence.and.are.usually.only.discovered.and.validated.through.high-resolution.
studies. like. x-ray. crystallography. (Westhof. and. Fritsch. 2000).. Because. of. the. various.
complex. 3D. conformations. and. interactions. possible. for. RNA,. successful. modeling.
frequently. requires. advanced. computer. analysis.. However,. despite. the. huge. number.
of. possible. interactions,. techniques. for. RNA. modeling. and. analysis. typically. focus.
on. the. canonical. and. wobble. base. pairings,. leaving. an. incomplete. picture. for. the. full.
folding. interactions. of. most. RNA. molecules,. necessitating. further. bench. work.. More.
complicated. structures. such. as. pseudoknots. (Figure. 5.1c). are. also. quite. dificult. to.
model.without.structural.data.
The.highest.order.of.RNA.interactions.is.the.quaternary.structure,.consisting.of.numer-
ous.interactions,.including.RNA-RNA,.RNA-protein,.RNA-DNA,.and.even.RNA-small.
molecule. interactions. (Figure. 5.2).. These. interactions. rely. on. the. secondary. and. tertiary.
structures.to.create.highly.speciic.binding..Two.of.the.most.well-characterized.biological.
examples. of. the. RNA-protein. (RNP). interaction. (Figure. 5.2a). are. the. histone. stem-loop.
(Williams. and. Marzluff. 1995),. a. ubiquitous. RNA. hairpin. found. in. the. mRNA. of. most.
histone. messages,. and. the. iron-response. element. (Hentze. et. al.. 1987). found. in. multiple.
cellular. RNAs. involved. in. iron. metabolism.. In. both. cases,. a. protein. (the. histone. stem-
loop.binding.protein.or.iron-response.element.binding.protein).binds.speciically.to.this.
hairpin-loop.structure.to.regulate.RNA..Creative.use.of.these.hybrid.complexes.will.help.
deine.the.future.of.RNA.nanotechnology.
There.are.numerous.examples.of.RNA.binding.to.small.ligands.from.organic.molecules.
such.as.amino.acids,.guanosine,.or.cofactors.to.large.dye.molecules.such.as.ethidium.bro-
mide. or. SYBR. gold,. which. are. used. as. RNA-imaging. agents. (Chow. and. Bogdan. 1997)..
Creating.a.type.of.artiicial.hybrid.association.with.RNA.is.like.creating.a.key.to.a.con-
stantly. changing. dynamic. lock.. This. is. where. powerful. techniques. like. SELEX. (system-
atic.evolution.of.ligands.by.exponential.enrichment).(Tuerk.and.Gold.1990).have.proven.
useful..In.SELEX,.a.large.library.of.the.intended.molecules,.typically.oligonucleotides,.is.
selected.against.a.target.(e.g.,.protein).over.several.rounds.of.positive.and.negative.selec-
tion..This.technique.can.be.used.for.creating.hybrid.functional.networks.and.not.just.for.
elaborate.RNA.architecture.production.
(a)
(b)
(c)
Figure 5.2
(See companion CD for color igure.)
.Quaternary.(4°).RNA.interactions..Tertiary.structures.give.RNA.remark-
able.speciic.binding.capabilities,.allowing.for.formation.of.numerous.quaternary.structures..(a).Protein.bind-
ing.speciically.to.hairpin.structures.in.RNA..(b).
Trans
.RNA-RNA.binding.as.demonstrated.through.hairpin.
interactions,.forming.a.“kissing.complex.”.(c).Sequence-speciic.binding.of.small.ligands,.resulting.in.binding.
events.or.conformational.changes.
