Chemical modification of ribonucleic acid. A direct study by carbon-13 nuclear magnetic resonance spectroscopy

Chang, Chin-Jer; Lee, Chi-Gen

doi:10.1021/bi00512a046

Cited by 15 publications

(9 citation statements)

References 26 publications

(17 reference statements)

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“…Here, we have shown that [ 14 C]MeI treatment of tRNA introduces 1-meG lesions, and that these lesions are repaired by AlkB. Previous studies have shown that 1-meG is the major methylation product obtained by MeI treatment of guanosine under basic conditions (28), and that other methylating agents can induce 1-meG in RNA and DNA in vitro (16)(17)(18) and in vivo (22). We also attempted to introduce 1-meG residues in DNA by treatment of a G-rich oligonucleotide with [ 14 C] MeI, but were unsuccessful (P. Ø. Falnes and R. F. Johansen, unpublished data).…”

Section: Discussionmentioning

confidence: 77%

“…1-meA and 3-meC are methylated at N-atoms that are involved in Watson-Crick base pairing of the corresponding normal bases, and this is also the case for 1-meG and 3-meT. Although less prevalent than 1-meA and 3-meC, both 3-meT and 1-meG have been reported to be introduced upon treatment of DNA or RNA with alkylating agents, both in vitro (16)(17)(18)(19)(20) and in vivo (21,22). In the present study, we report that both 1-meG and 3-meT can be repaired by AlkB proteins from humans and bacteria.…”

Section: Introductionmentioning

confidence: 99%

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Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins

Falnes

2004

Nucleic Acids Research

101

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The Escherichia coli AlkB protein repairs 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions in DNA and RNA by oxidative demethylation, a reaction requiring ferrous iron and 2-oxoglutarate as cofactor and co-substrate, respectively. Here, we have studied the activity of AlkB proteins on 3-methylthymine (3-meT) and 1-methylguanine (1-meG), two minor lesions which are structurally analogous to 1-meA and 3-meC. AlkB as well as the human AlkB homologues, hABH2 and hABH3, were all able to demethylate 3-meT in a DNA oligonucleotide containing a single 3-meT residue. Also, 1-meG lesions introduced by chemical methylation of tRNA were efficiently removed by AlkB. Unlike 1-meA and 3-meC, nucleosides or bases corresponding to 1-meG or 3-meT did not stimulate the uncoupled, AlkB-mediated decarboxylation of 2-oxoglutarate. Our data show that 3-meT and 1-meG are repaired by AlkB, but indicate that the recognition of these substrates is different from that in the case of 1-meA and 3-meC.

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Section: Discussionmentioning

confidence: 77%

Section: Introductionmentioning

confidence: 99%

Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins

Falnes

2004

Nucleic Acids Research

101

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“…These adducts can be readily detected by reverse-transcription analysis, as the modification at the Watson-Crick face induces premature cDNA termination or, in the MaP strategy, incorporation of a noncomplementary nucleotide. While generally ignored, DMS also is known to methylate both G and U residues (Lawley and Shah 1972;Kusḿierek and Singer 1976;Chang and Lee 1981;Ashworth et al 1985). For example, DMS readily reacts with the N7 of the imidazole ring of G; however, N7 adducts do not efficiently interfere with conventional reverse transcription and are thus not typically detected in probing experiments (Ehresmann et al 1987).…”

Section: Resultsmentioning

confidence: 99%

“…For example, DMS readily reacts with the N7 of the imidazole ring of G; however, N7 adducts do not efficiently interfere with conventional reverse transcription and are thus not typically detected in probing experiments (Ehresmann et al 1987). G nucleotides can also be methylated at the N1 and N3 positions, and U nucleotides can be methylated at the N3 position, likely through mechanisms that involve transient base deprotonation or tautomerization (Lawley and Shah 1972;Kusḿierek and Singer 1976;Chang and Lee 1981;Ashworth et al 1985). These modifications are at the Watson-Crick face and thus should be detectable by reverse-transcription analysis.…”

Section: Resultsmentioning

confidence: 99%

Direct identification of base-paired RNA nucleotides by correlated chemical probing

Krokhotin

Mustoe

Weeks

et al. 2016

RNA

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Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner. While probing data are highly useful for inferring overall RNA secondary structure, these data do not directly measure through-space base-pairing interactions. We recently introduced an approach for single-molecule correlated chemical probing with dimethyl sulfate (DMS) that measures RNA interaction groups by mutational profiling (RING-MaP). RING-MaP experiments reveal diverse through-space interactions corresponding to both secondary and tertiary structure. Here we develop a framework for using RING-MaP data to directly and robustly identify canonical base pairs in RNA. When applied to three representative RNAs, this framework identified 20%-50% of accepted base pairs with a <10% false discovery rate, allowing detection of 88% of duplexes containing four or more base pairs, including pseudoknotted pairs. We further show that base pairs determined from RING-MaP analysis significantly improve secondary structure modeling. RING-MaP-based correlated chemical probing represents a direct, experimentally concise, and accurate approach for detection of individual base pairs and helices and should greatly facilitate structure modeling for complex RNAs.

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“…2). Resonance signals attributable to the phosphate-bound methyl group of GMP-OMe [18,19] were easily spotted, as there were no similar counterparts in the absence of methanol. In addition, the effect induced by the methyl group in the resonances of certain GMP nuclei gave rise to upfield/downfield shifts such that some of the homologous nuclei in GMP and GMP-OMe could be distinguished from each other despite the proximity of their respective signals.…”

Section: Spectroscopic Analysismentioning

confidence: 99%

Methanol esterification reactions catalyzed by snake venom and bovine intestinal 5′‐nucleotide phosphodiesterases

García-Díaz

Авалос

Cameselle

1991

European Journal of Biochemistry

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It is not known whether the enzymes 5'-nucleotide phosphodiesterase/nucleotide pyrophosphatase (EC 3.1.4.1/ EC 3.6.1.9) catalyze the transfer of nucleotides to acceptors other than water. We have investigated the action of snake venom and bovine intestinal mucosa phosphodiesterases on nucleoside 5'-polyphosphates in the presence of methanol. In those conditions, GTP was converted by snake venom phosphodiesterase to a mixture of GMP and another compound with a different retention time in reverse-phase high-performance liquid chromatography. That compound, by ultraviolet, 'H-and I3C-nuclear magnetic resonance spectroscopic analysis, and by enzyme analysis, was characterized as the methyl ester of GMP (GMP-OMe). The molar fraction [GMP-OMe]/ [GMP + GMP-OMe] formed was higher than the molar fraction of methanol as a solvent in reaction mixtures.Similar reactions took place at comparable rates with snake venom and bovine intestinal mucosa phosphodiesterases using several nucleoside 5'-polyphosphates as substrates. The ability of 5'-nucleotide phosphodiesterases to catalyze transfer reactions to a non-water acceptor is relevant to the mechanism of the enzymes, to their use as analytical tools, and to their possible use/role in the preparativelin vivo synthesis of nucleotide esters.Phosphodiesterase I or 5'-nucleotide phosphodiesterase, and nucleotide pyrophosphatase are overlapping names which, in many cases, can be applied to the same enzyme. For example, snake venom phosphodiesterase (SVP) [l], 5'-nucleotide phosphodiesterase from bovine intestinal mucosa (BIMP) [2, 31, and liver nucleotide pyrophosphatase [4, 51 show both types of activity: they are phosphohydrolases removing 5'-nucleotides from phosphodiester and phosphoanhydride linkages. The mechanism of action of SVP [6 -91 and BIMP [lo-141 involves the formation of a nucleotidyl intermediate, covalently bound to the enzyme, which is transferred to a molecule of water, yielding the 5'-nucleotide hydrolysis product.The possibility that 5'-nucleotide phosphodiesterase/ nucleotide pyrophosphatase enzymes catalyze 5'-nucleotidyl transfers to acceptors other than water has been little explored. On the one hand, there are quotations in the literature indicating that transfer reactions of BIMP have been searched for but not detected [13, 151. In addition, the participation of rat liver nucleotide pyrophosphatase in the transfer of 5'-adenylyl groups to glycerol had been deemed possible, but it was disregarded on kinetic grounds [16]. On the other hand, there is an early report studying the action of Habu snake venom and pig kidney phosphodiesterase preparations on the artificial substrate ethyl-phospho-p-nitrophenol [17]. In that case, incubations in the presence of glycerol or ethylenglycol yielded a lower molar amount of ethyl phosphate (measured as phosphatase-labile phosphate) than of p-nitrophenol, an indication that transfers to alcohol acceptors could be taking place, although the esterification products were not directly detected [17]. Altogether, the scarce a...

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Chemical modification of ribonucleic acid. A direct study by carbon-13 nuclear magnetic resonance spectroscopy

Cited by 15 publications

References 26 publications

Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins

Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins

Direct identification of base-paired RNA nucleotides by correlated chemical probing

Methanol esterification reactions catalyzed by snake venom and bovine intestinal 5′‐nucleotide phosphodiesterases

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