Selenium derivatization of nucleic acids for crystallography

Jiang, Jiansheng; Sheng, Jia; Carrasco, Nicolas; Huang, Zhen

doi:10.1093/nar/gkl1070

Cited by 64 publications

(84 citation statements)

References 41 publications

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“…Out of these three sequences, only the U267-SeCH 3 DIS variant produced diffraction quality crystals. Interestingly, as reported previously for a 29-SeCH 3 -labeled DNA duplex (Jiang et al 2007), these Sederivatized crystals grew significantly faster and larger than crystals with unmodified RNA, leading to an improvement in the diffraction limit (Table 1). Poorly diffracting crystals and spherulites were obtained with the U266-SeCH 3 DIS RNA, and no crystals were found for the U270-SeCH 3 DIS sequence (Fig.…”

Section: Resultssupporting

confidence: 78%

“…29-methylseleno (29-SeCH 3 ) labeling of nucleic acids has been developed as an alternative to two broadly used phasing techniques, to the halogenation of pyrimidines and to soaking crystals in heavy atom salt solutions Teplova et al 2002;Carrasco et al 2004;Jiang et al 2007;Pallan and Egli 2007). The 29-SeCH 3 -labeling method, suited for the determination of RNA structures, relies on the crystallization of RNA molecules that have natural nucleoside(s) substituted for their 29-SeCH 3 -modified counterparts during chemical RNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

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A fast selenium derivatization strategy for crystallization and phasing of RNA structures

Oliéric¹,

Rieder²,

Lang³

et al. 2009

RNA

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Site-specific 29-methylseleno RNA labeling is a promising tool for tackling the phase problem in RNA crystallography. We have developed an efficient strategy for crystallization and structure determination of RNA and RNA/protein complexes based on preliminary crystallization screening of 29-OCH 3 -modified RNA sequences, prior to the replacement of 29-OCH 3 groups with their 29-SeCH 3 counterparts. The method exploits the similar crystallization properties of 29-OCH 3 -and 29-SeCH 3 -modified RNAs and has been successfully validated for two test cases. In addition, our data show that 29-SeCH 3 -modified RNA have an increased resistance to X-ray radiolysis in comparison with commonly used 5-halogen-modified RNA, which permits collection of experimental electron density maps of remarkable quality.

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Section: Resultssupporting

confidence: 78%

Section: Introductionmentioning

confidence: 99%

A fast selenium derivatization strategy for crystallization and phasing of RNA structures

Oliéric¹,

Rieder²,

Lang³

et al. 2009

RNA

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“…However, since the chemical and enzymatic incorporation of halogens is primarily limited to the 5-position of pyrimidine nucleosides (such as 5-BrdU as a mimic of T) [33] [34], the lack of multiple choices of derivatization positions has limited the usefulness of the halogen derivatization. Moreover, the possible basestacking disruption, hydration pattern alteration, and backbone perturbation [43] can also limit the applications of the halogen derivatization. In addition, recent reports have indicated that the light sensitivity and instability of halogen derivatives can lead to their decomposition after exposure to UV irradiation, let alone long-time X-ray irradiation during the diffraction data collection [44] [45].…”

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confidence: 99%

Selenium Derivatization of Nucleic Acids for X‐Ray Crystal‐Structure and Function Studies

Sheng

Huang

2010

Chemistry & Biodiversity

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It is estimated that over two thirds of all new crystal structures of proteins are determined via the protein selenium derivatization (selenomethionine (Se-Met) strategy). This selenium derivatization strategy via MAD (multi-wavelength anomalous dispersion) phasing has revolutionized protein X-ray crystallography. Through our pioneer research, similarly, Se has also been successfully incorporated into nucleic acids to facilitate the X-ray crystal-structure and function studies of nucleic acids. Currently, Se has been stably introduced into nucleic acids by replacing nucleotide O-atom at the positions 2', 4', 5', and in nucleobases and non-bridging phosphates. The Se derivatization of nucleic acids can be achieved through solid-phase chemical synthesis and enzymatic methods, and the Se-derivatized nucleic acids (SeNA) can be easily purified by HPLC, FPLC, and gel electrophoresis to obtain high purity. It has also been demonstrated that the Se derivatization of nucleic acids facilitates the phase determination via MAD phasing without significant perturbation. A growing number of structures of DNAs, RNAs, and protein-nucleic acid complexes have been determined by the Se derivatization and MAD phasing. Furthermore, it was observed that the Se derivatization can facilitate crystallization, especially when it is introduced to the 2'-position. In addition, this novel derivatization strategy has many advantages over the conventional halogen derivatization, such as more choices of the modification sites via the atom-specific substitution of the nucleotide O-atom, better stability under X-ray radiation, and structure isomorphism. Therefore, our Se-derivatization strategy has great potentials to provide rational solutions for both phase determination and high-quality crystal growth in nucleic-acid crystallography. Moreover, the Se derivatization generates the nucleic acids with many new properties and creates a new paradigm of nucleic acids. This review summarizes the recent developments of the atomic site-specific Se derivatization of nucleic acids for structure determination and function study. Several applications of this Se-derivatization strategy in nucleic acid and protein research are also described in this review.

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“…We were the first to synthesize Se-derivatized nucleoside phosphoramidites and incorporate them into nucleic acids by solid-phase synthesis. For convenience, recently we have coined the abbreviation SeNA [51], which refers to Se-derivatized nucleic acid. So far, we and other research groups have introduced Se into both DNA and RNA chemically and enzymatically by replacement of selected O with Se at a variety of positions, including O-atoms in the 5'-and 2'-positions, the non-bridging phosphate backbones, and nucleobases [38 -53].…”

mentioning

confidence: 99%

“…The Se-derivatized DNA sequences crystallize under a broader range of buffer conditions [51 -53], and generally have a faster crystal growth rate with higher diffraction quality when compared with the native structure and traditional halogen derivatization. Furthermore, by comparing the Se-derivatization with the conventional Br-derivatization, we found that the Brderivatization caused local perturbations, such as the backbone rotation, the H 2 Onetworking disruption, and the hydrate pattern alteration [51].…”

mentioning

confidence: 99%

Biochemistry of Selenium‐Derivatized Naturally Occurring and Unnatural Nucleic Acids

Caton-Williams

Huang

2008

Chemistry & Biodiversity

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Selenium (Se) can provide unique biochemical and biological functions, and properties to macromolecules, including protein and RNA. Although Se has not yet been found in DNA, identification of the presence of Se in natural tRNAs has led to discovery of the naturally occurring 2-selenouridine and 5-[(methylamino)methyl]-2-selenouridine (mnm 5 se 2 U). The Se-atoms at C(2) of the modified uridines are introduced by 2-selenouridine synthase via displacement of the S-atoms in the corresponding 2-thiouridine nucleotides of the tRNAs, and selenophosphate is used as the Se donor. The research indicated that mnm 5 se 2 U is located at the first or wobble position of the anticodons in several bacterial tRNAs, including tRNA Lys , tRNA Glu , and tRNA Gln . The 2-seleno functionality on this modified nucleotide probably improves the translation accuracy and/or efficiency. These observations in vivo suggest that the presence of Se can provide natural RNAs with useful properties to better function and survival. To further investigate the biochemical and structural properties of Se-derivatized nucleic acids (SeNA), we have pioneered chemical and enzymatic synthesis of Se-derivatized nucleic acids, and introduced Se into both RNA and DNA at a variety of positions by atom-specific replacement of oxygen. This review outlines the recent advancements in chemical and biochemical syntheses, and studies of SeNAs, and their potential applications in structural and functional investigation of nucleic acids and their protein complexes.

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Selenium derivatization of nucleic acids for crystallography

Cited by 64 publications

References 41 publications

A fast selenium derivatization strategy for crystallization and phasing of RNA structures

A fast selenium derivatization strategy for crystallization and phasing of RNA structures

Selenium Derivatization of Nucleic Acids for X‐Ray Crystal‐Structure and Function Studies

Biochemistry of Selenium‐Derivatized Naturally Occurring and Unnatural Nucleic Acids

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