Nucleic acid X-ray crystallography via direct selenium derivatization

Lin, Lina; Sheng, Jia; Huang, Zhen

doi:10.1039/c1cs15020k

Cited by 67 publications

(40 citation statements)

References 67 publications

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“…We have also observed previously that the 2′-Se-facilitator does not cause significant local and global structure perturbation (13,14,26,31). The 5-MeO locates in the major groove of the A-form helix (Figure 2B).…”

Section: Resultssupporting

confidence: 82%

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

Sheng¹,

Gan²,

Soares³

et al. 2012

Nucleic Acids Research

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Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation.

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Section: Resultssupporting

confidence: 82%

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

Sheng¹,

Gan²,

Soares³

et al. 2012

Nucleic Acids Research

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“…Selenium has the X-ray K absorption edge at a wavelength of 0.979 Å and exhibits a significant anomalous signal, which can be very conveniently used for phasing by the Multi- or Single-wavelength Anomalous Diffraction (MAD12 or SAD13) approaches at any of the available synchrotron beam lines. Selenium can be also chemically introduced into nucleic acids1415.…”

mentioning

confidence: 99%

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Luo

2016

Sci Rep

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Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be inserted into protein crystals in the form of selenourea (SeC(NH2)2), by adding the crystalline powder of selenourea into mother liquor or cryo-solution with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as donors. Selenourea has different chemical properties than heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules.

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“…Excitingly, after a single-oxygen atom replacement with selenium, we have observed for the first time the color RNAs (light yellow) as well as color RNA crystals (dark yellow). The color property of the Se U-RNAs is unique and has great potentials in RNA visualization, detection, spectroscopic study and crystallography of RNAs and protein-RNA complexes and interactions, demonstrating the usefulness of selenium-derivatized nucleic acids (SeNA) (36,37) in structural biology. In addition, both the anomalous phasing and molecular replacement approaches result in the identical crystal structures.…”

Section: Introductionmentioning

confidence: 99%

Structural insights of non-canonical U•U pair and Hoogsteen interaction probed with Se atom

Sheng

Gan

Soares

et al. 2013

Nucleic Acids Research

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Unlike DNA, in addition to the 2′-OH group, uracil nucleobase and its modifications play essential roles in structure and function diversities of non-coding RNAs. Non-canonical U•U base pair is ubiquitous in non-coding RNAs, which are highly diversified. However, it is not completely clear how uracil plays the diversifing roles. To investigate and compare the uracil in U-A and U•U base pairs, we have decided to probe them with a selenium atom by synthesizing the novel 4-Se-uridine (SeU) phosphoramidite and Se-nucleobase-modified RNAs (SeU-RNAs), where the exo-4-oxygen of uracil is replaced by selenium. Our crystal structure studies of U-A and U•U pairs reveal that the native and Se-derivatized structures are virtually identical, and both U-A and U•U pairs can accommodate large Se atoms. Our thermostability and crystal structure studies indicate that the weakened H-bonding in U-A pair may be compensated by the base stacking, and that the stacking of the trans-Hoogsteen U•U pairs may stabilize RNA duplex and its junction. Our result confirms that the hydrogen bond (O4…H-C5) of the Hoogsteen pair is weak. Using the Se atom probe, our Se-functionalization studies reveal more insights into the U•U interaction and U-participation in structure and function diversification of nucleic acids.

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Nucleic acid X-ray crystallography via direct selenium derivatization

Cited by 67 publications

References 67 publications

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Structural insights of non-canonical U•U pair and Hoogsteen interaction probed with Se atom

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