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Bioorg Med Chem Lett. 2017 Jun 1;27(11):2506-2509. doi: 10.1016/j.bmcl.2017.03.096. Epub 2017 Apr 1.

Identification of acylation products in SHAPE chemistry.

Author information

1
PPSM, CNRS, Institut d'Alembert, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du P(t) Wilson, F-94235 Cachan, France.
2
LAMBE, CNRS, Université d'Evry Val d'Essonne, CEA, Université Paris-Saclay, F-91025 Evry, France.
3
LBPA, CNRS, Institut d'Alembert, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du P(t) Wilson, F-94235 Cachan, France.
4
PPSM, CNRS, Institut d'Alembert, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du P(t) Wilson, F-94235 Cachan, France. Electronic address: joanne.xie@ens-cachan.fr.

Abstract

SHAPE chemistry (selective 2'-hydroxyl acylation analyzed by primer extension) has been developed to specifically target flexible nucleotides (often unpaired nucleotides) independently to their purine or pyrimidine nature for RNA secondary structure determination. However, to the best of our knowledge, the structure of 2'-O-acylation products has never been confirmed by NMR or X-ray data. We have realized the acylation reactions between cNMP and NMIA under SHAPE chemistry conditions and identified the acylation products using standard NMR spectroscopy and LC-MS/MS experiments. For cAMP and cGMP, the major acylation product is the 2'-O-acylated compound (>99%). A trace amount of N-acylated cAMP has also been identified by LC-UV-MS2. While for cCMP, the isolated acylation products are composed of 96% of 2'-O-acylated, 4% of N,O-diacylated, and trace amount of N-acylated compounds. In addition, the characterization of the major 2'-O-acylated compound by NMR showed slight differences in the conformation of the acylated sugar between the three cyclic nucleotides. This interesting result should be useful to explain some unexpected reactivity of the SHAPE chemistry.

KEYWORDS:

Acylation reaction; LC–UV–MS(2); NMR; RNA; SHAPE chemistry; cNMP

PMID:
28400233
DOI:
10.1016/j.bmcl.2017.03.096
[Indexed for MEDLINE]

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