Synthesis and crystal structure study of 2′-Se-adenosine-derivatized DNA

Abstract

The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids. Selenium can serve as an excellent anomalous scattering center to solve the phase problem, which is one of the two major bottlenecks in macromolecule X-ray crystallography. The other major bottleneck is crystallization. It has been demonstrated that the incorporated selenium functionality at the 2′-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation. Furthermore, it was observed that the 2′-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality. Herein, we describe a convenient synthesis of the 2′-Se-adenosine phosphoramidite, and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2′-Se-A derivatization. The 3D structure of 2′-Se-A-DNA decamer [5′-GTACGCGT(2′-Se-A)C-3′] 2 was determined at 1.75 Å resolution, the 2′-Se-functionality points to the minor groove, and the Se-modified and native structures are virtually identical. Moreover, we have observed that the 2′-Se-A modification can greatly facilitate the crystal growth with high diffraction quality. In conjunction with the crystallization facilitation by the 2′-Se-U and 2′-Se-T, this novel observation on the 2′-Se-A functionality suggests that the 2′-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly. selenium derivatization, nucleic acid, adenosine, X-ray crystallography, structure determination

Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization

“…To further confirm that this 5-TePh modification does not cause obvious structure perturbations, we have carried out the crystallization by using our 2′-Se modification strategy to facilitate the crystal growth ( 46–48 ). The modified DNA (5′-G- 2′-Se dU-G- Te T-ACAC-3′) was designed, synthesized and purified.…”

The importance of fitting in: conformational preference of selenium 2′ modifications in nucleosides and helical structures

“…Recent data has shown that the nature of the base of the modified nucleotide is not a determining factor for crystal growth, as enhanced crystal growth was also observed for other 2’-methylseleno-modified nucleotides (Salon et al, 2010; Sheng & Huang, 2010; Sheng, Salon, Gan, & Huang, 2010). As exhibited by DNA oligonucleotides containing embedded ribose moieties, localized A-type perturbations in overall B-type DNA oligonucleotides can be observed in solution structures, yet this mixed conformation is rarely seen in crystal structures, which favor longer-lived species.…”

Chemical and structural biology of nucleic acids and protein-nucleic acid complexes for novel drug discovery

“…Currently, given the emerging structural information of nucleic acids and their protein complexes, structure-based drug design will soon be at the heart of nucleic acid-targeting drug discovery. Recently, our laboratory pioneered and has developed the selenium derivatization of nucleic acid (SeNA) technologies [176][177][178][179][180][181], which have significantly facilitated crystal structure and function studies of nucleic acids and protein-nucleic acid complexes. With the continuous research efforts on chemical and structural biology of nucleic acids, the understandings on nucleic acid folding, structure, recognition and catalysis will be significantly further advanced.…”