2H9S

Crystal Structure of Homo-DNA and Nature's Choice of Pentose over Hexose in the Genetic System


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.

Egli, M.Pallan, P.S.Pattanayek, R.Wilds, C.J.Lubini, P.Minasov, G.Dobler, M.Leumann, C.J.Eschenmoser, A.

(2006) J.Am.Chem.Soc. 128: 10847-10856

  • DOI: 10.1021/ja062548x

  • PubMed Abstract: 
  • An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that ...

    An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.


    Organizational Affiliation

    Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA. martin.egli@vanderbilt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3'A,B8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
XAD
Query on XAD
A, B
DNA LINKINGC11 H16 N5 O6 PDA
XCT
Query on XCT
A, B
DNA LINKINGC10 H16 N3 O7 PDC
XTH
Query on XTH
A, B
DNA LINKINGC11 H17 N2 O8 PDT
XGU
Query on XGU
A, B
DNA LINKINGC11 H16 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 38.940α = 90.00
b = 38.940β = 90.00
c = 133.850γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-06-11 
  • Released Date: 2006-12-12 
  • Deposition Author(s): Egli, M., Pallan, P.S.

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance