3Q61

3'-Fluoro Hexitol Nucleic Acid DNA Structure

• PDB DOI: https://doi.org/10.2210/pdb3Q61/pdb
• NAKB: 3Q61

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-12-30 Released: 2012-01-18 
• Deposition Author(s): Seth, P.R., Allerson, C.R., Prakash, T.P., Siwkowski, A., Berdeja, A., Yu, J., Pallan, P.S., Watt, A.T., Gaus, H., Bhat, B., Egli, M., Swayze, E.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.209 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides.

Egli, M., Pallan, P.S., Allerson, C.R., Prakash, T.P., Berdeja, A., Yu, J., Lee, S., Watt, A., Gaus, H., Bhat, B., Swayze, E.E., Seth, P.P.

(2011) J Am Chem Soc 133: 16642-16649

• PubMed: 21919455 
• DOI: https://doi.org/10.1021/ja207086x
• Primary Citation of Related Structures:  
  3Q61


• PubMed Abstract: 
  

  The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F···H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py)···H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.

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Organizational Affiliation: 

Department of Biochemistry, School of Medicine, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37232, USA. [e-mail]

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 6.15 kDa 
• Atom Count: 484 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*TP*AP*(F3H)P*AP*CP*GP*C)-3')	A, B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.209 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.014	α = 90
b = 43.134	β = 90
c = 45.507	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
MOLREP	phasing
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Seth, P.R., Allerson, C.R., Prakash, T.P., Siwkowski, A., Berdeja, A., Yu, J., Pallan, P.S., Watt, A.T., Gaus, H., Bhat, B., Egli, M., Swayze, E.E.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description