Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 7.45 kDa 
• Atom Count: 565 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique hybrid chains: 1

 5VXQ

X-Ray crystallography structure of the parallel stranded duplex formed by 5-rA5-dA-rA5

• PDB DOI:  https://doi.org/10.2210/pdb5VXQ/pdb
• NDB: 5VXQ

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


• Deposited: 2017-05-23 Released: 2017-08-16 
• Deposition Author(s): Xie, J., Chen, Y., Wei, X., Kozlov, G., Gehring, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.160 
• R-Value Work: 0.129 

Literature

Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

Copp, W., Denisov, A.Y., Xie, J., Noronha, A.M., Liczner, C., Safaee, N., Wilds, C.J., Gehring, K.

(2017) Nucleic Acids Res 45: 10321-10331

• PubMed: 28973475 
• DOI: https://doi.org/10.1093/nar/gkx713
• Primary Citation of Related Structures:  
  5TGG, 5VXQ


• PubMed Abstract: 
  

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability.

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Organizational Affiliation: 

Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*AP*AP*AP*AP*A)-D(P*A)-R(P*AP*AP*AP*AP*A)-3')	A, B	11	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NH4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.160 
• R-Value Work: 0.129 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.799	α = 90
b = 22.799	β = 90
c = 164.071	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Xie, J., Chen, Y., Wei, X., Kozlov, G., Gehring, K.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Database references
• Version 1.2: 2017-10-11
  Changes: Database references