2-Selenouridine triphosphate synthesis and Se-RNA transcription

Sun, Huiyan; Jiang, Shuhui; Caton-Williams, Julianne; Liu, Hehua; Huang, Zhen

doi:10.1261/rna.038075.112

Cited by 18 publications

(13 citation statements)

References 21 publications

(26 reference statements)

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“…Consequently, effective synthesis of a phosphoramidite derivative of suitably protected Se2U was developed, and numerous synthetic Se2U-RNAs were obtained for structural, physicochemical and functional studies [25,29,30]. Huang and co-workers, who pioneered the chemical synthesis of various Se-derivatives of nucleic acids [31], also developed enzymatic synthesis of Se2U-RNAs utilizing 2-selenouridine triphosphate (Se2UTP) and RNA transcription [32].…”

Section: Introductionmentioning

confidence: 99%

C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons

Leszczyńska

Cypryk

Gostyński

et al. 2020

IJMS

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5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1-3 were assessed to be significantly lower compared to their 2-thio-and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called "new wobble base pair", which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5 -NNG-3 synonymous codons, unlike their 2-thio-and 2-oxo-precursors, which preferentially read the 5 -NNA-3 codons. Thus, the interplay between the levels of U-, S2U-and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3 -A-and 3 -G-ending codons.

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Section: Introductionmentioning

confidence: 99%

C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons

Leszczyńska

Cypryk

Gostyński

et al. 2020

IJMS

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“… Natural N/A Sun et al. [101] Selenobiotin Phycomyces blakesleeanus Natural N/A Sum bui et al. [169] Boron Borophycin and structurally related compounds Nostoc spongiaeforme, Teredinibacter turnerae, etc.…”

Section: Halogenationmentioning

confidence: 99%

Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering

Reed

Alper

2018

Synthetic and Systems Biotechnology

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Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially) be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.

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“…Among all Se-derivatized nucleic acids, 2-Se-uridine is the only naturally occurring modification. Extensive experimental data show that the 2-seleno-modifiaction has high stability [11] as well as virtually identical structure to the native in RNA structure [12]. One economical and efficient method to incorporate multiple Se Us into a RNA molecule is through in vitro transcription, since this strategy is well established and favored by most biology laboratories.…”

Section: Introductionmentioning

confidence: 99%

Nucleic Acid Crystallography via Direct Selenium Derivatization: RNAs Modified with Se-Nucleobases

Sun

Jiang

Huang

2016

Methods in Molecular Biology

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Selenium-derivatized RNAs are powerful tools for structure and function studies of RNAs and their protein complexes. By taking the advantage of selenium modifications, researchers can determine novel RNA structures via convenient SAD and MAD phasing. As one of the naturally occurring tRNA modifications, 2-seleno-uridine, which presents almost exclusively at the wobble position of anticodon loop in various bacterial tRNAs (Ching et al., Proc Natl Acad Sci U S A 82:347, 1985; Dunin-Horkawicz et al., Nucleic Acids Res 34:D145–D149, 2006), becomes one of the most promising modifications for crystallographic studies. Our previous studies have demonstrated many unique properties of 2-seleno-uridine, including stability (Sun et al., RNA 19:1309–1314, 2013), minimal structural perturbation (Sun et al., Nucleic Acids Res 40:5171–5179, 2012), and enhanced base-pairing fidelity (Sun et al., Nucleic Acids Res 40:5171–5179, 2012). In this protocol, we present the efficient chemical synthesis of 2-seleno-uridine triphosphate (SeUTP) and the facile transcription and purification of SeU-containing RNAs (SeU-RNA).

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2-Selenouridine triphosphate synthesis and Se-RNA transcription

Cited by 18 publications

References 21 publications

C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons

C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons

Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering

Nucleic Acid Crystallography via Direct Selenium Derivatization: RNAs Modified with Se-Nucleobases

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