2AXB

Crystal Structure Analysis Of A 2-O-[2-(methoxy)ethyl]-2-thiothymidine Modified Oligodeoxynucleotide Duplex

Summary for 2AXB

• Entry DOI: 10.2210/pdb2axb/pdb
• Descriptor: 5'-D(*GP*CP*GP*TP*AP*(S2M)P*AP*CP*GP*C)-3') (2 entities in total)
• Functional Keywords: dna
• Total number of polymer chains: 2
• Total formula weight: 6270.30

Authors

Diop-Frimpong, B.,Prakash, T.P.,Rajeev, K.G.,Manoharan, M.,Egli, M. (deposition date: 2005-09-04, release date: 2005-11-01, Last modification date: 2024-02-14)

Primary citation

Diop-Frimpong, B.,Prakash, T.P.,Rajeev, K.G.,Manoharan, M.,Egli, M.
Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines.
Nucleic Acids Res., 33:5297-5307, 2005

PubMed Abstract: 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.

PubMed: 16170156
DOI: 10.1093/nar/gki823

Experimental method

X-RAY DIFFRACTION (1.61 Å)