1MLX | pdb_00001mlx

Crystal Structure Analysis of a 2'-O-[2-(Methylthio)-ethyl]-Modified Oligodeoxynucleotide Duplex

• PDB DOI: https://doi.org/10.2210/pdb1MLX/pdb
• NAKB: 1MLX

• Classification: DNA
• Mutation(s): No 


• Deposited: 2002-08-31 Released: 2002-12-04 
• Deposition Author(s): Prakash, T.P., Manoharan, M., Kawasaki, A.M., Fraser, A.S., Lesnik, E.A., Sioufi, N., Leeds, J.M., Teplova, M., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.144 (DCC) 
• R-Value Work: 
  0.136 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

2'-O-[2-(Methylthio)ethyl]-Modified Oligonucleotide: An Analogue of 2'-O-[2-(Methoxy)-ethyl]-Modified Oligonucleotide with Improved Protein Binding Properties and High Binding Affinity to Target RNA

Prakash, T.P., Manoharan, M., Kawasaki, A.M., Fraser, A.S., Lesnik, E.A., Sioufi, N., Leeds, J.M., Teplova, M., Egli, M.

(2002) Biochemistry 41: 11642-11648

• PubMed: 12269806 
• DOI: https://doi.org/10.1021/bi020264t
• Primary Citation Related Structures: 
  1MLX


• PubMed Abstract: 
  

  A novel 2'-modification, 2'-O-[2-(methylthio)ethyl] or 2'-O-MTE, has been incorporated into oligonucleotides and evaluated for properties relevant to antisense activity. The results were compared with the previously characterized 2'-O-[2-(methoxy)ethyl] 2'-O-MOE modification. As expected, the 2'-O-MTE modified oligonucleotides exhibited improved binding to human serum albumin compared to the 2'-O-MOE modified oligonucleotides. The 2'-O-MTE oligonucleotides maintained high binding affinity to target RNA. Nuclease digestion of 2'-O-MTE oligonucleotides showed that they have limited resistance to exonuclease degradation. We analyzed the crystal structure of a decamer DNA duplex containing the 2'-O-MTE modifcation. Analysis of the crystal structure provides insight into the improved RNA binding affinity, protein binding affinity and limited resistance of 2'-O-MTE modified oligonucleotides to exonuclease degradation.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Isis Pharmaceuticals, 2292 Faraday Ave, Carlsbad, CA 92008, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.27 kDa 
• Atom Count: 557 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*AP*SMTP*AP*CP*GP*C)-3'	A, B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.144 (DCC) 
• R-Value Work:  0.136 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.728	α = 90
b = 44.473	β = 90
c = 46.229	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-04 
Deposition Author(s): Prakash, T.P., Manoharan, M., Kawasaki, A.M., Fraser, A.S., Lesnik, E.A., Sioufi, N., Leeds, J.M., Teplova, M., Egli, M.

Revision History  

• Version 1.0: 2002-12-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations