2axb
From Proteopedia
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Crystal Structure Analysis Of A 2-O-[2-(methoxy)ethyl]-2-thiothymidine Modified Oligodeoxynucleotide Duplex
Overview
Substitution of oxygen atoms by sulfur at various locations in the nucleic, acid framework has led to analogs such as the DNA phosphorothioates and, 4'-thio RNA. The phosphorothioates are excellent mimics of DNA, exhibit, increased resistance to nuclease degradation compared with the natural, counterpart, and have been widely used as first-generation antisense, nucleic acid analogs for applications in vitro and in vivo. The 4'-thio, RNA analog exhibits significantly enhanced RNA affinity compared with RNA, and shows potential for incorporation into siRNAs. 2-Thiouridine (s2U) and, 5-methyl-2-thiouridine (m5s2U) are natural nucleotide analogs. s2U in tRNA, confers greater specificity of codon-anticodon interactions by, discriminating more strongly between A and G compared with U. 2-Thio, modification preorganizes the ribose and 2'-deoxyribose sugars for a, C3'-endo conformation, and stabilizes heteroduplexes composed of modified, DNA and complementary RNA. Combination of the 2-thio and sugar, 2'-O-modifications has been demonstrated to boost both thermodynamic, stability and nuclease resistance. Using the, 2'-O-[2-(methoxy)ethyl]-2-thiothymidine (m5s2Umoe) analog, we have, investigated the consequences of the replacement of the 2-oxygen by sulfur, for base-pair geometry and duplex conformation. The crystal structure of, the A-form DNA duplex with sequence GCGTAT*ACGC (T* = m5s2Umoe) was, determined at high resolution and compared with the structure of the, corresponding duplex with T* = m5Umoe. Notable changes as a result of the, incorporation of sulfur concern the base-pair parameter 'opening', an, improvement of stacking in the vicinity of modified nucleotides as, measured by base overlap, and a van der Waals interaction between sulfur, atoms from adjacent m5s2Umoe residues in the minor groove. The structural, data indicate only minor adjustments in the water structure as a result of, the presence of sulfur. The observed small structural perturbations, combined with the favorable consequences for pairing stability and, nuclease resistance (when combined with 2'-O-modification) render, 2-thiouracil-modified RNA a promising candidate for applications in RNAi.
About this Structure
2AXB is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines., Diop-Frimpong B, Prakash TP, Rajeev KG, Manoharan M, Egli M, Nucleic Acids Res. 2005 Sep 16;33(16):5297-307. Print 2005. PMID:16170156
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