3OZ5

S-Methyl Carbocyclic LNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA.

Seth, P.P.Allerson, C.R.Berdeja, A.Siwkowski, A.Pallan, P.S.Gaus, H.Prakash, T.P.Watt, A.T.Egli, M.Swayze, E.E.

(2010) J.Am.Chem.Soc. 132: 14942-14950

  • DOI: 10.1021/ja105875e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We show for the first time that it is possible to obtain LNA-like (Locked Nucleic Acid 1) binding affinity and biological activity with carbocyclic LNA (cLNA) analogs by replacing the 2'-oxygen atom in LNA with an exocyclic methylene group. Synthesis ...

    We show for the first time that it is possible to obtain LNA-like (Locked Nucleic Acid 1) binding affinity and biological activity with carbocyclic LNA (cLNA) analogs by replacing the 2'-oxygen atom in LNA with an exocyclic methylene group. Synthesis of the methylene-cLNA nucleoside was accomplished by an intramolecular cyclization reaction between a radical at the 2'-position and a propynyl group at the C-4' position. Only methylene-cLNA modified oligonucleotides showed similar thermal stability and mismatch discrimination properties for complementary nucleic acids as LNA. In contrast, the close structurally related methyl-cLNA analogs showed diminished hybridization properties. Analysis of crystal structures of cLNA modified self-complementary DNA decamer duplexes revealed that the methylene group participates in a tight interaction with a 2'-deoxyribose residue of the 5'-terminal G of a neighboring duplex, resulting in the formation of a CH...O type hydrogen bond. This indicates that the methylene group retains a negative polarization at the edge of the minor groove in the absence of a hydrophilic 2'-substituent and provides a rationale for the superior thermal stability of this modification. In animal experiments, methylene-cLNA antisense oligonucleotides (ASOs) showed similar in vivo activity but reduced toxicity as compared to LNA ASOs. Our work highlights the interchangeable role of oxygen and unsaturated moieties in nucleic acid structure and emphasizes greater use of this bioisostere to improve the properties of nucleic acids for therapeutic and diagnostic applications.


    Organizational Affiliation

    Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1891 Rutherford Road, Carlsbad, California 92008, USA. pseth@isisph.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*TP*AP*(UMX)P*AP*CP*GP*C)-3')A,B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
B
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UMX
Query on UMX
A, B
DNA linkingC12 H17 N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.465α = 90.00
b = 44.112β = 90.00
c = 45.954γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description