ISDA

Deposition Date 2011-12-07

Release Date 2012-02-08

Last Version Date 2023-09-13

Entry Detail

PDB ID:

3V07

Keywords:

DNA

Title:

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

Biological Source:

Source Organism:

(Taxon ID: ) (Taxon ID: )

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.24 Å

R-Value Free:

0.20

R-Value Work:

0.15

R-Value Observed:

0.16

Space Group:

P 21 21 21

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*GP*TP*AP*(F6H)P*AP*CP*GP*C)-3')
Chain IDs:A, B
Chain Length:10
Number of Molecules:2
Biological Source:

Primary Citation

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.Show

Biochemistry 51 7 9 (2012)

PMID: 22229409 DOI: 10.1021/bi201810r

Abstact

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.

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