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PDBsum entry 1dhh
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DNA-RNA hybrid
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PDB id
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1dhh
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PDB id:
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DNA-RNA hybrid
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Title:
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Nmr solution structure of the DNA duplex containing DNA/RNA hybrid region, d(gg)r(agau)d(gac)/d(gtcatctcc)
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Structure:
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DNA/RNA (5'-d( Gp G)-r(p Ap Gp Ap U)-d(p Gp Ap C)-3'). Chain: a. Synonym: dhd. Engineered: yes. Other_details: crystallization conditions\: ph 7.0, 298k, 100mm nacl, 50mm na phosphate, 3mm edta. DNA (5'-d( Gp Tp Cp Ap Tp Cp Tp Cp C)-3'). Chain: b. Synonym: dhd.
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Source:
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Synthetic: yes. Other_details: a substrate of rnase h. Other_details: a substrate of rnase h
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NMR struc:
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1 models
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Authors:
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T.Nishizaki,S.Iwai,T.Ohkubo,C.Kojima,H.Nakamura,Y.Kyogoku,E.Ohtsuka
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Key ref:
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T.Nishizaki
et al.
(1996).
Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC).
Biochemistry,
35,
4016-4025.
PubMed id:
DOI:
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Date:
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18-Oct-95
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Release date:
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03-Apr-96
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Headers
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References
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G-G-A-G-A-U-G-A-C
9 bases
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G-T-C-A-T-C-T-C-C
9 bases
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DOI no:
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Biochemistry
35:4016-4025
(1996)
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PubMed id:
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Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC).
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T.Nishizaki,
S.Iwai,
T.Ohkubo,
C.Kojima,
H.Nakamura,
Y.Kyogoku,
E.Ohtsuka.
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ABSTRACT
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The solution structures of two DNA duplexes containing a DNA*RNA hybrid region
at different sites, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) (DHD, where D and H
represent the DNA and DNA x RNA hybrid segments, respectively) and
d(GGAGA)r(UGAC) x d(GTCATCTCC) (DDH), were determined by nuclear magnetic
resonance spectroscopy to clarify the structural features of the D-H and H-D
junctions. All proton-proton distances were derived from the NOESY spectra, with
mixing times of 45 ms, and the restrained molecular dynamics were carried out
starting from the typical A- and B-form conformations. Both duplexes were
converged from the respective initial structures into structures with RMSD
values of less than 1.0 angstrom. These structures were subjected to full
relaxation matrix refinement to produce the final structures. In the case of the
D-H junction, where the ribonucleotide was linked to the 3'-end of the DNA, the
H2' and H2" signals of the deoxynucleotide overlapped completely, and the
ribonucleotide had a H1'-H2' coupling constant larger than that of the normal
C3'-endo sugar pucker. The dihedral angles, the pseudorotation phase angles, and
the helical parameters changed at the H-D junction, but not at the D-H junction.
A detailed comparison of the two duplexes revealed the structural heterogeneity
between the DNA segment and the DNA x RNA hybrid region and the transitions at
the junctions.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Matsugami,
T.Ohyama,
M.Inada,
N.Inoue,
N.Minakawa,
A.Matsuda,
and
M.Katahira
(2008).
Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.
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Nucleic Acids Res,
36,
1805-1812.
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PDB code:
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S.T.Hsu,
M.T.Chou,
and
J.W.Cheng
(2000).
The solution structure of [d(CGC)r(aaa)d(TTTGCG)](2): hybrid junctions flanked by DNA duplexes.
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Nucleic Acids Res,
28,
1322-1331.
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Y.Xiong,
and
M.Sundaralingam
(1998).
Crystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)-r(GAAGAAGAA).
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Structure,
6,
1493-1501.
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PDB code:
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A.Lebrun,
and
R.Lavery
(1997).
Unusual DNA conformations.
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Curr Opin Struct Biol,
7,
348-354.
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L.S.Kappen,
Z.Xi,
and
I.H.Goldberg
(1997).
Effect of ribonucleotide substitution on nucleic acid bulge recognition by neocarzinostatin.
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Bioorg Med Chem,
5,
1221-1227.
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T.Nishizaki,
S.Iwai,
E.Ohtsuka,
and
H.Nakamura
(1997).
Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center.
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Biochemistry,
36,
2577-2585.
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PDB code:
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Where a reference describes a PDB structure, the PDB
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shown on the right.
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