5DER | pdb_00005der

RNA oligonucleotide containing (R)-C5'-ME-2'F U

PDB DOI: https://doi.org/10.2210/pdb5DER/pdb
NAKB: 5DER

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2015-08-25 Released: 2016-06-29
Deposition Author(s): Harp, J.M., Egli, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.274 (Depositor), 0.273 (DCC)
R-Value Work:
0.257 (Depositor), 0.255 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides.

Kel In, A.V., Zlatev, I., Harp, J., Jayaraman, M., Bisbe, A., O Shea, J., Taneja, N., Manoharan, R.M., Khan, S., Charisse, K., Maier, M.A., Egli, M., Rajeev, K.G., Manoharan, M.

(2016) J Org Chem 81: 2261-2279

PubMed: 26940174 Search on PubMed
DOI: https://doi.org/10.1021/acs.joc.5b02375
Primary Citation Related Structures:
5D8T, 5DEK, 5DER

PubMed Abstract:
Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease resistance of oligonucleotides (ONs). Here, we report the synthesis of enantiomerically pure (R)- and (S)-5'-C-methyl (C5'-Me) substituted nucleosides and their incorporation into ONs. These modifications generally resulted in a decrease in thermal stability of oligonucleotide (ON) duplexes in a manner dependent on the stereoconfiguration at C5' with greater destabilization characteristic of (R)-epimers. Enhanced stability against snake venom phosphodiesterase resulted from modification of the 3'-end of an ON with either (R)- or (S)-C5'-Me nucleotides. The (S)-isomers with different 2'-substituents provided greater resistance against 3'-exonucleases than the corresponding (R)-isomers. Crystal structure analyses of RNA octamers with (R)- or (S)-5'-C-methyl-2'-deoxy-2'-fluorouridine [(R)- or (S)-C5'-Me-2'-FU, respectively] revealed that the stereochemical orientation of the C5'-Me and the steric effects that emanate from the alkyl substitution are the dominant determinants of thermal stability and are likely molecular origins of resistance against nucleases. X-ray and NMR structural analyses showed that the (S)-C5'-Me epimers are spatially and structurally more similar to their natural 5' nonmethylated counterparts than the corresponding (R)-epimers.