The NMR
structure
s of
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s/bichaw/46/i06/eqn/bi061350me10001.gif"> and
sub
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s/bichaw/46/i06/eqn/bi061350me10002.gif"> are reported. The internal loop,
sub
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s/bichaw/46/i06/eqn/bi061350me10003.gif">, i
s about 2 kcal/mol more
stable than
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s/bichaw/46/i06/eqn/bi061350me10004.gif"> at 37
s/entitie
s/deg.gif">C. The duplexe
s a
ssemble into
similar globalfold
s characterized by the formation of tandem
sheared GA pair
s. The different
stabilitie
s of the loop
s areaccompained by difference
s in the local
structure of the clo
sing GU pair
s. In the
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s/bichaw/46/i06/eqn/bi061350me10005.gif"> internal loop,the GU pair
s form canonical wobble configuration
s with two hydrogen bond
s, wherea
s in
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s/bichaw/46/i06/eqn/bi061350me10006.gif">, theGU pair
s form a
single hydrogen bond involving the amino group, GH22, and the carbonyl group, UO4.Thi
s pairing i
s similar to the GU clo
sing pair of the 690 hairpin loop found in
E. coli 16S rRNA. The
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s/bichaw/46/i06/eqn/bi061350me10007.gif"> and
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s/bichaw/46/i06/eqn/bi061350me10008.gif">
structure
s reveal how the
subtle interplay between
stacking and hydrogen bondingdetermine
s sequence dependent conformation and thermodynamic
stability. Thu
s, thi
s work provide
sstructural and thermodynamic benchmark
s for theoretician
s in the ongoing effort to under
stand the
sequencedependence of RNA phy
sicochemical propertie
s.