Insights from Crystallographic Studies into the Structural and Pairing Properties of Nucleic Acid Analogs and Chemically Modified DNA and RNA Oligonucleotides

Egli, Martin; Pallan, Pradeep S.

doi:10.1146/annurev.biophys.36.040306.132556

Cited by 57 publications

(42 citation statements)

References 103 publications

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“…X-ray crystallography is one of the most powerful approaches for 3D structure determination of macromolecules, including nucleic acids, proteins, and their complexes [1][2][3][4]. The 3D structure study at the atomic level provides novel and detailed insights into the structure-function relationships, regulations, and molecular interactions of many biological processes.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2010

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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

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Section: Introductionmentioning

confidence: 99%

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

et al. 2010

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“…X-Ray crystallography is one of the most powerful tools for nucleic acid structure studies, which allows detailed understandings of biological processes at the atomic level [6] [20 -30], including mechanisms of replication, transcription and translation, and their regulation, DNA damage and repairing, DNA -drug and RNAdrug complexes, catalytic RNAs, riboswitch function, and nucleic acid -protein interactions. Moreover, crystallographic research provides fundamental insights into nucleic acid hydration, cation interaction, stereoelectronic effects, and conformational preorganization [31]. Structural and functional understanding of nucleic acids provides guiding principles for gene expression control and drug discovery.…”

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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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“…Over the past decades, a large number of artificial oligonucleotides were synthesized with modifications occurring in the phosphodiester, sugar, or nucleobase moiety, which were shown to be resistant to chemical degradation and were able to selectively hybridize to target nucleic acids with strong affinity [57,58]. They were proved to be capable of hybridizing with the complementary DNA or RNA sequence with substantial increased thermal stabilities compared to the parent DNA: DNA or DNA: RNA duplexes, which made themselves promising candidates for clinical applications [59].…”

Section: Artificially Modified Oligonucleotidementioning

confidence: 99%