3V06

Crystal structure of S-6'-Me-3'-fluoro hexitol nucleic acid

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2011-12-07 Released: 2012-02-08 
  • Deposition Author(s): Pallan, P.S., Egli, M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report



Literature

Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid.

Pallan, P.S.Yu, J.Allerson, C.R.Swayze, E.E.Seth, P.Egli, M.

(2012) Biochemistry 51: 7-9

  • DOI: 10.1021/bi201810r
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Locked nucleic acid (LNA) analogues with 2',4'-bridged sugars show promise in antisense applications. S-5'-Me-LNA has high RNA affinity, and modified oligonucleotides show weakened immune stimulation in vivo. Conversely, an R-5'-methyl group dramatic ...

    Locked nucleic acid (LNA) analogues with 2',4'-bridged sugars show promise in antisense applications. S-5'-Me-LNA has high RNA affinity, and modified oligonucleotides show weakened immune stimulation in vivo. Conversely, an R-5'-methyl group dramatically lowers RNA affinity. To test the effects of S- and R-6'-methyl groups on 3'-fluoro hexitol nucleic acid (FHNA) stability, we synthesized S- and R-6'-Me-FHNA thymidine and incorporated them into oligo-2'-deoxynucleotides. As with LNA, S-6'-Me is stabilizing whereas R-6'-Me is destabilizing. Crystal structures of 6'-Me-FHNA-modified DNAs explain the divergent consequences for stability and suggest convergent origins of these effects by S- and R-6'-Me (FHNA) [-5'-Me (LNA and RNA)] substituents.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*TP*AP*(F5H)P*AP*CP*GP*C)-3')A, B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SR
Query on SR

Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.879α = 90
b = 45.222β = 90
c = 46.598γ = 90
Software Package:
Software NamePurpose
MD2data collection
CCP4model building
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-12-07 
  • Released Date: 2012-02-08 
  • Deposition Author(s): Pallan, P.S., Egli, M.

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release