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1hg9

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Solution structure of DNA:RNA hybrid

Structural highlights

1hg9 is a 2 chain structure with sequence from Synthetic construct. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

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.

Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity.,Bondensgaard K, Petersen M, Singh SK, Rajwanshi VK, Kumar R, Wengel J, Jacobsen JP Chemistry. 2000 Aug 4;6(15):2687-95. PMID:10985717^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bondensgaard K, Petersen M, Singh SK, Rajwanshi VK, Kumar R, Wengel J, Jacobsen JP. Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity. Chemistry. 2000 Aug 4;6(15):2687-95. PMID:10985717

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1hg9"

@@ Line 1: / Line 1: @@
-==SOLUTION STRUCTURE OF DNA:RNA HYBRID==
-<StructureSection load='1hg9' size='340' side='right' caption='[[1hg9]], [[NMR_Ensembles_of_Models | 40 NMR models]]' scene=''>
+==Solution structure of DNA:RNA hybrid==
+<StructureSection load='1hg9' size='340' side='right'caption='[[1hg9]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1hg9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HG9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1HG9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1hg9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HG9 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hhw|1hhw]], [[1hhx|1hhx]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hg9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1hg9 RCSB], [http://www.ebi.ac.uk/pdbsum/1hg9 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hg9 OCA], [https://pdbe.org/1hg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hg9 RCSB], [https://www.ebi.ac.uk/pdbsum/1hg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hg9 ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 14: / Line 15: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1hg9" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bondensgaard, K]]
+[[Category: Large Structures]]
-[[Category: Jacobsen, J P]]
+[[Category: Synthetic construct]]
-[[Category: Petersen, M]]
+[[Category: Bondensgaard K]]
-[[Category: Wengel, J]]
+[[Category: Jacobsen JP]]
-[[Category: Antisense]]
+[[Category: Petersen M]]
-[[Category: Dna]]
+[[Category: Wengel J]]
-[[Category: Dna rna hybrid]]
-[[Category: Dna-rna hybrid]]
-[[Category: Dna/rna chimeric hybrid duplex]]
-[[Category: Hybrid]]
-[[Category: Locked nucleic acid]]
-[[Category: Rna]]
-[[Category: Rnase h]]

1hg9

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Current revision

Solution structure of DNA:RNA hybrid

Structural highlights

Publication Abstract from PubMed

References

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