1yb9
Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(N,N-dimethylaminooxy)ethyl] Thymidine (T*)
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OverviewOverview
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.
About this StructureAbout this Structure
1YB9 is a Protein complex structure of sequences from [1] with SPM as ligand. Full crystallographic information is available from OCA.
ReferenceReference
Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2'-O-ribonucleic acid modifications., Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M, Biochemistry. 2005 Jun 28;44(25):9045-57. PMID:15966728
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