page_title: Nucleic acid structure determination
section_title: Kethoxal, glyoxal and derivatives
hierarchical_section_title: Nucleic acid structure determination / Chemical probing / Kethoxal, glyoxal and derivatives
caption_attribution_description: English: This depicts the mechanism by which glyoxal derivatives can react with guanines at N1 and N2. From: Mitchell D, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC. 2018. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA 24: 114–124.
context_page_description: Experimental approaches of determining the structure of nucleic acids, such as RNA and DNA, can be largely classified into biophysical and biochemical methods. Biophysical methods use the fundamental physical properties of molecules for structure determination, including X-ray crystallography, NMR and cryo-EM. Biochemical methods exploit the chemical properties of nucleic acids using specific reagents and conditions to assay the structure of nucleic acids. Such methods may involve chemical probing with specific reagents, or rely on native or analogue chemistry. Different experimental approaches have unique merits and are suitable for different experimental purposes.
context_section_description: Some 1,2-dicarbonyl compounds are able to react with single-stranded guanine (G) at N1 and N2, forming a five-membered ring adduct at the Watson-Crick face.
  1,1-Dihydroxy-3-ethoxy-2-butanone, also known as kethoxal, has a structure related to 1,2-dicarbonyls, and was the first in this category used extensively for the chemical probing of RNA. Kethoxal causes the modification of guanine, specifically altering the N1 and the exocyclic amino group (N2) simultaneously by covalent interaction.
  Glyoxal, methylglyoxal, and phenylglyoxal, which all carry the key 1,2-dicarbonyl moiety, all react with free guanines similar to kethoxal, and can be used to probe unpaired guanine bases in structured RNA. Due to their chemical properties, these reagents can permeated readily into cells and can therefore be used to assay RNAs in their native cellular environments.
caption: Mechanism of reaction between 1,2-dicarbonyls and guanine.[34]
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