3V07: Crystal Structure Of R-6'-Me-3'-Fluoro Hexitol Nucleic Acid

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.
PDB ID: 3V07Download
MMDB ID: 97116
PDB Deposition Date: 2011/12/7
Updated in MMDB: 2012/02
Experimental Method:
x-ray diffraction
Resolution: 1.24  Å
Source Organism:
Biological Unit for 3V07: dimeric; determined by author and by software (PISA)
Molecular Components in 3V07
Label Count Molecule
Nucleotide(1 molecule)
DNA (5'-d(*gp*cp*gp*tp*ap*(f6h)p*ap*cp*gp*c)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB