1H0Q

NMR solution structure of a fully modified locked nucleic acid (LNA) hybridized to RNA

• PDB DOI: https://doi.org/10.2210/pdb1H0Q/pdb
• NAKB: 1H0Q

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


• Deposited: 2002-06-27 Released: 2003-07-17 
• Deposition Author(s): Rasmussen, J., Petersen, M., Nielsen, K.E., Kumar, R., Wengel, J., Jacobsen, J.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 

Literature

NMR Studies of Fully Modified Locked Nucleic Acid (Lna) Hybrids: Solution Structure of an Lna:RNA Hybrid and Characterization of an Lna:RNA Hybrid

Nielsen, K.E., Rasmussen, J., Kumar, R., Wengel, J., Jacobsen, J.P., Petersen, M.

(2004) Bioconjug Chem 15: 449

• PubMed: 15149171 
• DOI: https://doi.org/10.1021/bc034145h
• Primary Citation of Related Structures:  
  1H0Q


• PubMed Abstract: 
  

  LNA is a bicyclic nucleic acid analogue that contains one or more 2'-O,4'-C methylene linkage(s), which effectively locks the furanose ring in a C3'-endo conformation. We report here the NMR solution structure of a nonamer LNA:RNA hybrid and a structural characterization of a nonamer LNA:DNA hybrid, where the LNA strands are composed entirely of LNA nucleotides. This is the first structural characterization of fully modified LNA oligonucleotides. The high-resolution structure reveals that the LNA:RNA hybrid adopts an almost canonical A-type duplex morphology. The helix axis is almost straight and the duplex geometry is regular. This shows that fully modified LNA oligomers can hybridize with complementary RNA and form duplexes within the Watson-Crick framework. The LNA:DNA hybrid structurally resembles an RNA:DNA hybrid as shown by determination of deoxyribose sugar puckers and analysis of NOESY NMR spectra.

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Organizational Affiliation: 

Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.79 kDa 
• Atom Count: 390 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5-D(*(LKC)P*(TLN)P*(LCG)P*(LCA)P*(TLN)P*(LCA)P* (TLN)P*(LCG)P*(LCC))-3	A	9	N/A

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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-17 
Deposition Author(s): Rasmussen, J., Petersen, M., Nielsen, K.E., Kumar, R., Wengel, J., Jacobsen, J.P.

Revision History  

• Version 1.0: 2003-07-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance