Chemical probing of RNA with the hydroxyl radical at single-atom resolution
Azad, Robert N.
Jain, Swapan S.
Tullius, Thomas D.
MetadataShow full item record
Citation (published version)Shakti Ingle, Robert N Azad, Swapan S Jain, Thomas D Tullius. 2014. "Chemical probing of RNA with the hydroxyl radical at single-atom resolution." Nucleic Acids Research, Volume 42, Issue 20, pp. 12758 - 12767 (10). https://doi.org/10.1093/nar/gku934
While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5′-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5′-aldehyde. We conclude that hydroxyl radical abstracts a 5′-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5′ deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2′-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple.
Rights© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Showing items related by title, author, creator and subject.
Contribution of leaf specular reflection to canopy reflectance under black soil case using stochastic radiative transfer model Yang, Bin; Knyazikhin, Yuri; Zhao, Haimeng; Ma, Yuzhong (Elsevier Science BV, 2018-12-15)Numerous canopy radiative transfer models have been proposed based on the assumption of “ideal bi-Lambertian leaves” with the aim of simplifying the interactions between photons and vegetation canopies. This assumption may ...
Petroff, A.; Murphy, J.G.; Thomas, S.C.; Geddes, Jeffrey A. (PERGAMON-ELSEVIER SCIENCE LTD, 2018-10-01)Aerosol fluxes were measured by eddy-correlation for 8 weeks of the summer and fall of 2011 above a temperate broadleaf forest in central Ontario, Canada. These size-resolved measurements apply to particles with optical ...
Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska West, Catherine; Hofman, Courtney A.; Ebbert, Steve; Martin, John; Shirazi, Sabrina; Dunning, Samantha; Maldonado, Jesus E. (WILEY, 2017-10-01)The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed ...