Biological Assembly 1  

 3D View: Structure

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.59 kDa 
• Atom Count: 370 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 2

1HG9

Solution structure of DNA:RNA hybrid

• DOI: 10.2210/pdb1HG9/pdb
• NDB: 1HG9

• Classification: DNA-RNA HYBRID
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2000-12-13 Released: 2002-01-02 
• Deposition Author(s): Petersen, M., Bondensgaard, K., Wengel, J., Jacobsen, J.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 40 

Literature

Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity.

Bondensgaard, K., Petersen, M., Singh, S.K., Rajwanshi, V.K., Kumar, R., Wengel, J., Jacobsen, J.P.

(2000) Chemistry 6: 2687-2695

• PubMed: 10985717 
• DOI: 10.1002/1521-3765(20000804)6:15<2687::aid-chem2687>3.0.co;2-u
• Primary Citation of Related Structures:  
  1HG9


• PubMed Abstract: 
  

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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Related Citations: 

• The Conformations of Locked Nucleic Acids (Lna)
  Petersen, M., Nielsen, C.B., Nielsen, K.E., Jensen, G.A., Bondensgaard, K., Singh, S.K., Rajwanshi, V.K., Koshkin, A.A., Dahl, B.M., Wengel, J., Jacobsen, J.P.
  (2000) J Mol Recognit 13: 44

• Locked Nucleic Acid (Lna) Recognition of RNA: NMR Solution Structures of Lna:RNA Hybrids
  Petersen, M., Bondensgaard, K., Wengel, J., Jacobsen, J.P.
  (2002) J Am Chem Soc 124: 5974

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Organizational Affiliation: 

Department of Chemistry, University of Southern Denmark Odense University.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5- D(*CP*TP*GP*AP*TP*AP*TP*GP*C) -3	A	9	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3	B	9	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 40 
• OLDERADO: 1HG9 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-12-13 
• Released Date: 2002-01-02 
Deposition Author(s): Petersen, M., Bondensgaard, K., Wengel, J., Jacobsen, J.P.

Revision History  

• Version 1.0: 2002-01-02
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references, Other, Source and taxonomy