2H05

Br Derivitation of A-DNA Octamer GTG(Ubr)ACAC

Summary for 2H05

• Entry DOI: 10.2210/pdb2h05/pdb
• Related: 1Z7I 2DLJ 2GPX
• Descriptor: 5'-D(*GP*TP*GP*(BRU)P*AP*CP*AP*C)-3' (2 entities in total)
• Functional Keywords: br-dna, se-dna, se-br-dna, dna
• Total number of polymer chains: 1
• Total formula weight: 2491.49

Authors

Jiang, J.,Sheng, J.,Huang, Z. (deposition date: 2006-05-14, release date: 2006-05-23, Last modification date: 2023-08-30)

Primary citation

Jiang, J.,Sheng, J.,Carrasco, N.,Huang, Z.
Selenium derivatization of nucleic acids for crystallography.
Nucleic Acids Res., 35:477-485, 2007

PubMed Abstract: The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 A resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 A). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 A resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native and Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.

PubMed: 17169989
DOI: 10.1093/nar/gkl1070

Experimental method

X-RAY DIFFRACTION (1.8 Å)