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1dhh

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{{STRUCTURE_1dhh| PDB=1dhh | SCENE= }}
{{STRUCTURE_1dhh| PDB=1dhh | SCENE= }}
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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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===NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC)===
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==Overview==
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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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{{ABSTRACT_PUBMED_8672435}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DHH OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DHH OCA].
==Reference==
==Reference==
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[[Category: Dna/rna hybrid in dna duplex]]
[[Category: Dna/rna hybrid in dna duplex]]
[[Category: Nmr]]
[[Category: Nmr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:51:12 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 23:04:21 2008''

Revision as of 20:04, 30 June 2008

Image:1dhh.png

Template:STRUCTURE 1dhh

NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC)

Template:ABSTRACT PUBMED 8672435

About this Structure

Full experimental information is available from OCA.

Reference

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)., Nishizaki T, Iwai S, Ohkubo T, Kojima C, Nakamura H, Kyogoku Y, Ohtsuka E, Biochemistry. 1996 Apr 2;35(13):4016-25. PMID:8672435

Page seeded by OCA on Mon Jun 30 23:04:21 2008

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