Matrix-assisted laser desorption/ionization mass spectrometry screening for pseudouridine in mixtures of small RNAs by chemical derivatization, RNase digestion and signature products

We have developed a method to screen for pseudouridines in complex mixtures of small RNAs using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). First, the unfractionated crude mixture of tRNAs is digested to completion with an endoribonuclease, such as RNase T1, and the digestion products are examined using MALDI-MS. Individual RNAs are identified by their signature digestion products, which arise through the detection of unique mass values after nuclease digestion. Next, the endonuclease digest is derivatized using N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), which selectively modifies all pseudouridine, thiouridine and 2-methylthio-6-isopentenyladenosine nucleosides. MALDI-MS determination of the CMCT-derivatized endonuclease digest reveals the presence of pseudouridine through a 252 Da mass increase over the underivatized digest. Proof-of-concept experiments were conducted using a mixture of Escherichia coli transfer RNAs and endoribonucleases T1 and A. More than 80% of the expected pseudouridines from this mixture were detected using this screening approach, even on an unfractionated sample of tRNAs. This approach should be particularly useful in the identification of putative pseudouridine synthases through detection of their target RNAs and can provide insight into specific small RNAs that may contain pseudouridine.     

Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides,m(3)Psi and Psi

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.     

Synthesis of 15N-enriched pseudouridine derivatives

[reaction: see text]. A procedure for the chemical synthesis of [3-15N]-labeled pseudouridine and a methylated derivative was developed. A suitably protected pseudouridine precursor was nitrated at N3 followed by treatment with 15NH4Cl to afford the 15N-labeled product in six steps with a 20% yield. This methodology will allow for the production of RNAs with [3-15N]pseudouridine and [3-15N-methyl]pseudouridine at specific locations.     

高效毛细管电泳法检测尿液中的假尿嘧啶核苷

假尿嘧啶核苷（ψ）主要来自ｔＲＮＡ的降解,已证实在癌症患者尿液中排泄量异常,可以作为肿瘤诊断的极有用的标志物之一。用高效毛细管电泳法快速测定了人尿中的ψ,用涂层柱（２４ｃｍ×２５μｍｉ．ｄ．）及硼酸盐缓冲液,在线２００ｎｍ检测,可在４ｍｉｎ内使ψ与尿苷等及尿中其它内源物质完全分离。方法的日内、日间变异系数均小于４．０％,用磺基水杨酸作内标,以ψ浓度对相应的峰高或峰面积比定量得标准曲线（ｒ＞０．９９９０）,ψ最低检测限为４μｍｏｌ／Ｌ。     

Analysis of Pseudouridine by Fluorescence Spectrometry

Abstract

Fluorescence spectral properties of pseudouridine, an important biological indicator, have been measured for the first time in this study. The fluorescence quantum yield is maximal in aqueous solution with pH values above 9 with spectral properties characteristic of 5 alkyl substituted uracil derivatives. Chromatographic analysis shows the fluorescence is associated only with the pseudouridine peak. The concentration dependence of fluorescence is linear from 4 to 45 micromolar at pH 11.5. The excitation maximum is about 295 nm and the emission is broad with a maximum at about 390 nm. Addition of pseudouridine to urine extracts gives a linear increase in fluorescence with increasing pseudouridine concentration.     

Simultaneous determination of pseudouridine and creatinine in untreated urine by ion-pair liquid chromatography with diode-array ultraviolet detection

A simple procedure for the simultaneous determination of pseudouridine and creatinine in urine using ion-pair high-performance liquid chromatography with ultraviolet detection is described. It consists of simply diluting the filtered urine with mobile phase (1:20) followed by direct chromatographic injection. A single analysis takes only 10 min. This method has been applied to the analysis of urine samples from normal donors and patients with different types of cancer. The mean values, means, of the peak-area ratio of pseudouridine to creatinine were 61.79.10(-3) and 81.92.10(-3) for male and female normal donors, respectively. Out of twenty-five urine samples of patients with cancer examined, nineteen (all the forteen males included) had values higher than means + 2 sigma.     

高效液相色谱法测定人血清中假尿嘧啶核苷的浓度

应用反相高效液相色谱法测定人血清中假尿苷（ＰＤ）的含量,色谱柱为Ｎｏｖａ－ＰａｋＣ１８３．９ｍｍ×１５０ｍｍ,流动相为０．０４ｍｏｌ／Ｌ磷酸二氢钾缓冲液（ｐＨ４．０）,检测波长为２６３ｎｍ,线性范围为０．７～６．８μｍｏｌ／Ｌ,回收率为９３．５０％,日间误差ＣＶ＝３．１１％（ｎ＝６）。同时测定了部队体检正常人血清中ＰＤ的浓度,并用于临床观察肝炎、肾病、肺癌等多种疾病以及Ｈｅ－Ｎｅ激光治疗前后患者血中ＰＤ含量的变化。正常人血中ＰＤ的浓度无性别差异,成年人的正常值与文献一致。     

Probing conformational states of modified helix 69 in 50S ribosomes

The movement of the small ribosomal subunit (30S) relative to the large ribosomal subunit (50S) during translation is widely known, but many molecular details and roles of rRNA and proteins in this process are still undefined, especially in solution models. The functional relationship of modified nucleotides to ribosome activity is one such enigma. To better understand ribosome dynamics and the influence of modified nucleotides on such processes, the focus of this work was helix 69 of 23S rRNA, which contains three pseudouridine residues in its loop region. Ribosome probing experiments with dimethylsulfate revealed that specific base accessibilities and individual nucleotide conformations in helix 69 are influenced differently by pH, temperature, magnesium, and the presence of pseudouridine modifications.     

高效毛细管区带电泳测定人尿液中尿酸、肌酐和伪尿核苷的含量

报道了采用高效毛细管区带电泳技术直接将人尿液注入毛细管进行尿液中肌酐、尿酸及伪尿核苷含量测定的新方法。试验表明,以磷酸盐（ｐＨ６．１）作缓冲液,对人体尿液中肌酐、尿酸及伪尿核苷进行直接分析具有较高的灵敏度和较好的重复性。     

The pseudouridine synthases: revisiting a mechanism that seemed settled

RNA containing 5-fluorouridine, [f 5U]RNA, has been used as a mechanistic probe for the pseudouridine synthases, which convert uridine in RNA to its C-glycoside isomer, pseudouridine. Hydrated products of f 5U were attributed to ester hydrolysis of a covalent complex between an essential aspartic acid residue and f 5U, and the results were construed as strong support for a mechanism involving Michael addition by the aspartic acid residue. Labeling studies with [18O]water are now reported that rule out such ester hydrolysis in one pseudouridine synthase, TruB. The aspartic acid residue does not become labeled, and the hydroxyl group in the hydrated product of f 5U derives directly from solvent. The hydrated product, therefore, cannot be construed to support Michael addition during the conversion of uridine to pseudouridine, but the results do not rule out such a mechanism. A hypothesis is offered for the seemingly disparate behavior of different pseudouridine synthases toward [f 5U]RNA.     

Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation

Many nucleosides and their modified forms have been studied by mass spectrometry elaborating the detailed fragmentation pathways under MS2 and MS(n) conditions. Although the C-nucleoside pseudouridine has been fragmented and studied briefly, usually amongst many other nucleosides, it has not been investigated to the same extent as other nucleosides. In this report a number of different mass spectrometric techniques are applied to obtain a fuller picture of pseudouridine fragmentation. At the same time this study is used to compare different tandem mass spectrometric techniques, including a novel methodology utilising a quadrupole time-of-flight (Q-ToF) instrument for MS(n) analysis comparable with that available with an ion trap mass spectrometer.     

The products of 5-fluorouridine by the action of the pseudouridine synthase TruB disfavor one mechanism and suggest another

The pseudouridine synthase TruB handles 5-fluorouridine in RNA as a substrate, converting it into two isomeric hydrated products. Unexpectedly, the two products differ not in the hydrated pyrimidine ring but in the pentose ring, which is epimerized to arabinose in the minor product. This inversion of stereochemistry at C2' suggests that pseudouridine generation may proceed by a mechanism involving a glycal intermediate or that the previously proposed mechanism involving an acylal intermediate operates but with an added reaction manifold for 5-fluorouridine versus uridine. The arabino product strongly disfavors a mechanism involving a Michael addition to the pyrimidine ring.     

A chemical synthesis of the nucleoside 1-methylpseudouridine

A facile chemical synthesis of 1-methylpseudouridine has been accomplished by direct methylation of pseudouridine.     

Synthesis and biophysical characterization of tRNA(Lys,3) anticodon stem-loop RNAs containing the mcm(5)s(2)U nucleoside

[reaction: see text] Phosphoramidite reagents of the naturally occurring modified nucleosides mcm(5)s(2)U and mcm(5)U were synthesized and along with pseudouridine were incorporated into 17-nucleotide lysine tRNA anticodon stem-loop domains. Standard RNA phosphoramidite coupling chemistry allowed us to systematically investigate the thermodynamic effects of nucleoside modification and to correlate thermodynamic trends with qualitative structure effects seen by NMR spectroscopy.     

Nucleotides. Part XLII. The 2-dansylethoxycarbonyl (= 2-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}ethoxycarbonyl; dnseoc) group for protection of the 5′-hydroxy function in oligoribonucleotide synthesis

The 2-dansylethoxycarbonyl (Dnseoc) group was employed for protection of the 5′-hydroxy function in oligoribonucleotide synthesis by the phosphoramidite approach using the acid-labile tetrahydro-4-methoxy-2H-pyran-4-yl (Thmp) group for 2′-protection. The syntheses of monomeric building blocks, both phosphoramidites and nucleoside-functionalized supports, are described for the four common nucleosides adenosine, guanosine, cytidine, and uridine, and for the two modified minor nucleosides ribothymidine (= ribosylthymine) and pseudouridine.     

Highly regio- and stereoselective Michael addition of pseudouridine with propiolates: An efficient method for the synthesis of (E)-pseudouridine-N1-acrylate

The Michael addition of pseudouridine with various propiolates in the presence of DBU as a base and DMF as a solvent is described. It is noteworthy that the reaction is highly regio- and stereoselective and affords (E)-pseudouridine-N1-acrylate in good yields with high purities.     

Unexpected linear ion trap collision‐induced dissociation and Fourier transform ion cyclotron resonance infrared multi‐photon dissociation fragmentation of a hydrated C‐glycoside of 5‐fluorouridine formed by the action of the pseudouridine synthases RluA and TruB

As part of the investigation of the pseudouridine synthases, 5‐fluorouridine in RNA was employed as a mechanistic probe. The hydrated, rearranged product of 5‐fluorouridine was isolated as part of a dinucleotide and found to undergo unusual fragmentation during mass spectrometry, with the facile loss of HNCO from the product pyrimidine ring favored over phosphodiester bond rupture. Although the loss of HNCO from uridine and pseudouridine is well established, the pericyclic process leading to their fragmentation cannot operate with the saturated pyrimidine ring in the product of 5‐fluorouridine. Based on the MSⁿ results and calculations reported here, a new mechanism relying on the peculiar disposition of the functional groups of the product pyrimidine ring is proposed to account for the unusually facile fragmentation. Copyright © 2011 John Wiley & Sons, Ltd.