1WV6: X-Ray Structure Of The A-Decamer Gcgtatacgc With A Single 2'-O-Butyl Thymine In Place Of T6, Sr-Form

Citation:
Abstract
The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the development of RNAi therapeutics.
PDB ID: 1WV6Download
MMDB ID: 51949
PDB Deposition Date: 2004/12/11
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.55  Å
Source Organism:
Biological Unit for 1WV6: dimeric; determined by author
Molecular Components in 1WV6
Label Count Molecule
Nucleotide(1 molecule)
2
5'-d(*gp*cp*gp*tp*ap*(2bt)p*ap*cp*gp*c)-3'
Molecule annotation
Chemicals (5 molecules)
1
5
* Click molecule labels to explore molecular sequence information.

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