3BM0

Structure of DNA Octamer G(dUSe)G(5-SedU)ACAC

Summary for 3BM0

• Entry DOI: 10.2210/pdb3bm0/pdb
• Descriptor: 5'-D(*GP*(2'-Se-U)P*GP*(5-Se-U)P*AP*CP*AP*C)-3' (2 entities in total)
• Functional Keywords: selenium modified dna/rna, dna
• Total number of polymer chains: 1
• Total formula weight: 2584.54

Authors

Jiang, J.,SHeng, J.,Hassan, A.E.,Huang, Z. (deposition date: 2007-12-11, release date: 2008-06-10, Last modification date: 2024-02-21)

Primary citation

Hassan, A.E.,Sheng, J.,Jiang, J.,Zhang, W.,Huang, Z.
Synthesis and crystallographic analysis of 5-Se-thymidine DNAs.
Org.Lett., 11:2503-2506, 2009

PubMed Abstract: We investigated the possibility of the interaction of 5-CH(3) of thymidine and its 5'-phosphate backbone (C-H...O(-)-PO(3) interaction) in DNA via the insertion of the atomic probe (a selenium atom) into the exo-5-position of thymidine (5-Se-T). 5-Se-T was synthesized for the first time, via Mn(OAc)(3) assisted electrophilic addition of CH(3)SeSeCH(3) to 3',5'-di-O-benzoyl-2'-deoxyuridine. The 5-Se-T phosphoramidite was subsequently synthesized and incorporated into DNA in over 99% coupling yield. Biophysical and structural investigations of the 5-Se-T DNAs revealed that the Se-modified and nonmodified DNAs are virtually identical. In addition, the crystallographic analysis of a 5-Se-T DNA strongly suggests a hydrogen-bond formation between the 5-CH(3) and 5'-phosphate groups (CH(3)...PO(4)(-) interaction).

PubMed: 19469515
DOI: 10.1021/ol9004867

Experimental method

X-RAY DIFFRACTION (1.8 Å)