Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.48 kDa 
• Atom Count: 433 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 2

1OO7

DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES

• PDB DOI: 10.2210/pdb1OO7/pdb
• BMRB: 5781
• NDB: 1OO7

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


• Deposited: 2003-03-03 Released: 2003-11-11 
• Deposition Author(s): Gyi, J.I., Gao, D., Conn, G.L., Trent, J.O., Brown, T., Lane, A.N.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 4 
• Conformers Submitted: 4 
• Selection Criteria: all calculated structures submitted 

Literature

The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications

Gyi, J.I., Gao, D., Conn, G.L., Trent, J.O., Brown, T., Lane, A.N.

(2003) Nucleic Acids Res 31: 2683-2693

• PubMed: 12736318 
• DOI: 10.1093/nar/gkg356
• Primary Citation of Related Structures:  
  1OO7


• PubMed Abstract: 
  

The addition of the propynyl group at the 5 position of pyrimidine nucleotides is highly stabilising. We have determined the thermodynamic stability of the DNA.RNA hybrid r(GAAGAGAAGC)*d(GC(p)U(p)U(p)C(p)U(p) C(p)U(p)U(p)C) where p is the propynyl group at the 5 position and compared it with that of the unmodified duplex and the effects of methyl substitutions. The incorporation of the propyne group at the 5 position gives rise to a very large stabilisation of the hybrid duplex compared with the analogous 5-Me modification. The duplexes have been characterised by gel electrophoresis and NMR spectroscopy, which indicate that methyl substitutions have a smaller influence on local and global conformation than the propynyl groups. The increased NMR spectral dispersion of the propyne-modified duplex allowed a larger number of experimental restraints to be measured. Restrained molecular dynamics in a fully solvated system showed that the propyne modification leads to substantial conformational rearrangements stabilising a more A-like structure. The propynyl groups occupy a large part of the major groove and make favourable van der Waals interactions with their nearest neighbours and the atoms of the rings. This enhanced overlap may account at least in part for the increased thermodynamic stability. Furthermore, the simulations show a spine of hydration in the major groove as well as in the minor groove involving the RNA hydroxyl groups.

---

Related Citations: 

• Solution Structures of DNA.RNA Hybrids with Purine-Rich and Pyrimidine-Rich Strands: Comparison with the Homologous DNA and RNA Duplexes
  Gyi, J.I., Lane, A.N., Conn, G.L., Brown, T.
  (1998) Biochemistry 37: 73

• Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes
  Gyi, J.I., Conn, G.L., Lane, A.N., Brown, T.
  (1996) Biochemistry 35: 12538

---

Organizational Affiliation: 

Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'	A	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*(5PC)P*(PDU)P*(PDU)P*(5PC)P*(PDU)P*(5PC)P*(PDU)P*(PDU)P*C)-3'	B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 4 
• Conformers Submitted: 4 
• Selection Criteria: all calculated structures submitted 
• OLDERADO: 1OO7 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-03 
• Released Date: 2003-11-11 
Deposition Author(s): Gyi, J.I., Gao, D., Conn, G.L., Trent, J.O., Brown, T., Lane, A.N.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2021-07-28
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary