Articles | Volume 2, issue 2
Research article
14 Sep 2021
Research article |  | 14 Sep 2021

Rapid assessment of Watson–Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1H CEST

Bei Liu, Atul Rangadurai, Honglue Shi, and Hashim M. Al-Hashimi

Related subject area

Field: Liquid-state NMR | Topic: Applications – biological macromolecules
Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR
Sarah Kuschert, Martin Stroet, Yanni Ka-Yan Chin, Anne Claire Conibear, Xinying Jia, Thomas Lee, Christian Reinhard Otto Bartling, Kristian Strømgaard, Peter Güntert, Karl Johan Rosengren, Alan Edward Mark, and Mehdi Mobli
Magn. Reson., 4, 57–72,,, 2023
Short summary
Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine
Sreelakshmi Mekkattu Tharayil, Mithun C. Mahawaththa, Akiva Feintuch, Ansis Maleckis, Sven Ullrich, Richard Morewood, Michael J. Maxwell, Thomas Huber, Christoph Nitsche, Daniella Goldfarb, and Gottfried Otting
Magn. Reson., 3, 169–182,,, 2022
Short summary
Imatinib disassembles the regulatory core of Abelson kinase by binding to its ATP site and not by binding to its myristoyl pocket
Stephan Grzesiek, Johannes Paladini, Judith Habazettl, and Rajesh Sonti
Magn. Reson., 3, 91–99,,, 2022
Short summary
Localising nuclear spins by pseudocontact shifts from a single tagging site
Henry W. Orton, Elwy H. Abdelkader, Lydia Topping, Stephen J. Butler, and Gottfried Otting
Magn. Reson., 3, 65–76,,, 2022
Short summary
Localising individual atoms of tryptophan side chains in the metallo-β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites
Henry W. Orton, Iresha D. Herath, Ansis Maleckis, Shereen Jabar, Monika Szabo, Bim Graham, Colum Breen, Lydia Topping, Stephen J. Butler, and Gottfried Otting
Magn. Reson., 3, 1–13,,, 2022
Short summary

Cited articles

Afek, A., Shi, H., Rangadurai, A., Sahay, H., Senitzki, A., Xhani, S., Fang, M., Salinas, R., Mielko, Z., Pufall, M. A., Poon, G. M. K., Haran, T. E., Schumacher, M. A., Al-Hashimi, H. M., and Gordan, R.: DNA mismatches reveal conformational penalties in protein-DNA recognition, Nature, 587, 291–296,, 2020. 
Aishima, J., Gitti, R. K., Noah, J. E., Gan, H. H., Schlick, T., and Wolberger, C.: A Hoogsteen base pair embedded in undistorted B-DNA, Nucleic Acids Res., 30, 5244–5252, 2002. 
Alvey, H. S., Gottardo, F. L., Nikolova, E. N., and Al-Hashimi, H. M.: Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics, Nat. Commun., 5, 4786,, 2014. 
Baronti, L., Guzzetti, I., Ebrahimi, P., Friebe Sandoz, S., Steiner, E., Schlagnitweit, J., Fromm, B., Silva, L., Fontana, C., Chen, A. A., and Petzold, K.: Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA, Nature, 583, 139–144,, 2020. 
Ben Imeddourene, A., Zargarian, L., Buckle, M., Hartmann, B., and Mauffret, O.: Slow motions in A.T rich DNA sequence, Sci. Rep., 10, 19005,, 2020. 
Short summary
There is growing interest in mapping exchange dynamics between Watson–Crick and Hoogsteen conformations across different DNA contexts. However, current methods are ill-suited for measurements at a large scale because they require isotopically enriched samples. We report that Hoogsteen dynamics can be measured on unlabeled samples using 1H CEST experiments, which have higher throughput and lower cost relative to conventional methods and also provide new insights into Hoogsteen dynamics.