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

Oliéric, V.; Rieder, Ulrike; Lang, Kathrin; Serganov, Alexander; Schulze-Briese, Clemens; Micura, Ronald; Dumas, Philippe; Ennifar, Eric

doi:10.1261/rna.1499309

Cited by 47 publications

(56 citation statements)

References 35 publications

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“…Very recently, Ennifar and co-workers [45] have demonstrated that the 2'-OMe modification can be used for RNA-crystallization screening, considering the current high cost of Se derivatization. After identification of the crystallization conditions, the 2'-OMe group will be replaced with the 2'-SeMe functionality for the derivatization.…”

Section: 22mentioning

confidence: 99%

“…After identification of the crystallization conditions, the 2'-OMe group will be replaced with the 2'-SeMe functionality for the derivatization. In this work [45], U266, U267, and U270 sites of the DIS stem RNA were derivatized and screened. As a result, they found that the 2'-OMe and 2'-SeMe derivatized RNAs were comparable in terms of crystallization behavior and diffraction property.…”

Section: 22mentioning

confidence: 99%

“…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]. Furthermore, in many cases, the halogen derivatives cannot crystallize under the native conditions, and the derivative crystals often do not diffract as well as the native ones.…”

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confidence: 99%

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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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Section: 22mentioning

confidence: 99%

Section: 22mentioning

confidence: 99%

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confidence: 99%

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

Sheng

Huang

2010

Chemistry & Biodiversity

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“…Inspired by the convenient Se-derivatization of proteins, since 1998, Huang's research group has pioneered and developed the selenium derivatization of nucleic acids for X-ray crystallography (Carrasco et al 2001;Caton-Williams and Huang 2008;. We found that the selenium-derivatized RNAs and DNAs are stable and that the selenium derivatizations do not cause significant perturbation Salon et al 2007Salon et al , 2010Sheng et al 2007Sheng et al , 2011Caton-Williams and Huang 2008;Olieric et al 2009;Hassan et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Facile synthesis of nucleoside 5′-(α-P-seleno)-triphosphates and phosphoroselenoate RNA transcription

Lin¹,

Caton-Williams²,

Kaur³

et al. 2011

RNA

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Phosphoroselenoate RNA (PSe-RNA) is nuclease resistant and has great potentials in X-ray crystal structure and function studies of noncoding RNAs and protein-RNA interactions. In order to conveniently synthesize PSe-RNA via transcription, we have developed a one-pot synthetic method for the nucleoside 59-(a-P-seleno)-triphosphates (NTPaSe) analogs without protecting any functionality of the ribonucleosides. The NTPaSe diastereomers have been purified, fully characterized, and incorporated into RNAs by T7 RNA polymerase. The transcribed RNAs are diastereomerically pure, and the Se-derivatized ribozymes are generally active. Furthermore, we have established an affinity purification strategy by using immobilized boronate to conveniently purify NTPaSe analogs. Though the affinity-purified NTPaSe analogs are diastereomeric mixtures, they can be directly used in transcription without a significant impact on the transcription efficiency. Moreover, we found that the PSenucleotide is stable during polyacrylamide gel purification, indicating that the PSe-RNAs can be purified straightforwardly for crystal structural and functional studies.

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“…Furthermore, a series of selenium-containing nucleosides and oligonucleotides have been used for convenient phasing of X-ray crystallographic data. [11][12][13] Some methylseleno nucleosides were found to inhibit prostatic cancer cells growth. [14] Selenium has not been found in DNA, although its presence in natural uridines from tRNAs has been documented.…”

Section: Introductionmentioning

confidence: 99%

Synthesis of the First Selenium‐Containing Acyclic Nucleosides and Anomeric Spironucleosides from Carbohydrate Precursors

et al. 2009

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We report the synthesis of acyclic and spiranic imidazole-derived C-selenonucleosides. 5-Hydroxy-4-tetrahydroxybutyl imidazolidine-2-selones, a novel class of acyclic selenonucleosides, were transformed into (tetrahydroxybutylimidazol-2-yl)diselenide, by acetylation and chemoselective N-deacetylation with methanolic imidazole. Furthermore, the synthesis of a new class of conformationally restricted arabinoconfigured spironucleosides containing an imidazolidine-2-

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

Cited by 47 publications

References 35 publications

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

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

Facile synthesis of nucleoside 5′-(α-P-seleno)-triphosphates and phosphoroselenoate RNA transcription

Synthesis of the First Selenium‐Containing Acyclic Nucleosides and Anomeric Spironucleosides from Carbohydrate Precursors

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