(A) In MOHCA, copies of the RNA of interest that contain modified nucleotides—on average one per molecule—are made. These modified nucleotides produce hydroxyl groups that cleave the RNA and damage other nucleotides near to the modified nucleotide. A reverse transcriptase enzyme is used to generate DNA copies of the RNA molecules. This enzyme stops copying each RNA molecule at the point where it is cleaved or damaged. Therefore, sequencing these DNA fragments reveals the positions of nucleotides that are close to the modified nucleotide in the three-dimensional structure. This information is used to make a network of the interactions between all the nucleotides in the RNA (B). This network is then combined with algorithms that predict the secondary and tertiary structures to produce a single three-dimensional model of the tertiary structure (C). Image prepared by Nathan Baird using CodePen (codepen.io/blendmaster/full/uqibt) and structure 2YIE from the Protein Data Bank.