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PDBsum entry 1hg9
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DNA-RNA hybrid
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PDB id
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1hg9
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References listed in PDB file
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Key reference
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Title
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Structural studies of lna:RNA duplexes by nmr: conformations and implications for rnase h activity.
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Authors
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K.Bondensgaard,
M.Petersen,
S.K.Singh,
V.K.Rajwanshi,
R.Kumar,
J.Wengel,
J.P.Jacobsen.
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Ref.
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Chemistry, 2000,
6,
2687-2695.
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PubMed id
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Abstract
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We have used NMR and CD spectroscopy to study the conformations of modified
oligonucleotides (locked nucleic acid, LNA) containing a conformationally
restricted nucleotide (T(L)) with a 2'-O,4'-C-methylene bridge. We have
investigated two LNA:RNA duplexes, d(CTGAT(L)ATGC):r(GCAUAUCAG) and
d(CT(L)GAT(L)AT(L)GC):r(GCAUAUCAG), along with the unmodified DNA:RNA reference
duplex. Increases in the melting temperatures of +9.6 degrees C and +8.1 degrees
C per modification relative to the unmodified duplex were observed for these two
LNA:RNA sequences. The three duplexes all adopt right-handed helix conformations
and form normal Watson-Crick base pairs with all the bases in the anti
conformation. Sugar conformations were determined from measurements of scalar
coupling constants in the sugar rings and distance information derived from
1H-1H NOE measurements; all the sugars in the RNA strands of the three duplexes
adopt an N-type conformation (A-type structure), whereas the sugars in the DNA
strands change from an equilibrium between S- and N-type conformations in the
unmodified duplex towards more of the N-type conformation when modified
nucleotides are introduced. The presence of three modified T(L) nucleotides
induces drastic conformational shifts of the remaining unmodified nucleotides of
the DNA strand, changing all the sugar conformations except those of the
terminal sugars to the N type. The CD spectra of the three duplexes confirm the
structural changes described above. On the basis of the results reported herein,
we suggest that the observed conformational changes can be used to tune LNA:RNA
duplexes into substrates for RNase H: Partly modified LNA:RNA duplexes may adopt
a duplex structure between the standard A and B types, thereby making the RNA
strand amenable to RNase H-mediated degradation.
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Secondary reference #1
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Title
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The conformations of locked nucleic acids (lna).
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Authors
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M.Petersen,
C.B.Nielsen,
K.E.Nielsen,
G.A.Jensen,
K.Bondensgaard,
S.K.Singh,
V.K.Rajwanshi,
A.A.Koshkin,
B.M.Dahl,
J.Wengel,
J.P.Jacobsen.
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Ref.
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J Mol Recognit, 2000,
13,
44-53.
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PubMed id
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Secondary reference #2
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Title
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Locked nucleic acid (lna) recognition of RNA: nmr solution structures of lna:RNA hybrids.
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Authors
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M.Petersen,
K.Bondensgaard,
J.Wengel,
J.P.Jacobsen.
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Ref.
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J Am Chem Soc, 2002,
124,
5974-5982.
[DOI no: ]
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PubMed id
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Headers
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