Rapid assessment of Watson–Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino <sup>1</sup>H CEST
-
Published:2021-09-14
Issue:2
Volume:2
Page:715-731
-
ISSN:2699-0016
-
Container-title:Magnetic Resonance
-
language:en
-
Short-container-title:Magn. Reson.
Author:
Liu BeiORCID, Rangadurai Atul, Shi Honglue, Al-Hashimi Hashim M.
Abstract
Abstract. In duplex DNA, Watson–Crick A–T and G–C base pairs (bp's) exist in dynamic equilibrium with an alternative Hoogsteen conformation, which is low
in abundance and short-lived. Measuring how the Hoogsteen dynamics varies
across different DNA sequences, structural contexts and physiological
conditions is key for identifying potential Hoogsteen hot spots and for
understanding the potential roles of Hoogsteen base pairs in DNA recognition
and repair. However, such studies are hampered by the need to prepare
13C or 15N isotopically enriched DNA samples for NMR relaxation
dispersion (RD) experiments. Here, using SELective Optimized Proton
Experiments (SELOPE) 1H CEST experiments employing high-power
radiofrequency fields (B1 > 250 Hz) targeting imino protons,
we demonstrate accurate and robust characterization of Watson–Crick to
Hoogsteen exchange, without the need for isotopic enrichment of the DNA. For 13 residues in three DNA duplexes under different temperature and pH
conditions, the exchange parameters deduced from high-power imino 1H
CEST were in very good agreement with counterparts measured using
off-resonance 13C / 15N spin relaxation in the rotating frame
(R1ρ). It is shown that 1H–1H NOE effects which typically
introduce artifacts in 1H-based measurements of chemical exchange can
be effectively suppressed by selective excitation, provided that the
relaxation delay is short (≤ 100 ms). The 1H CEST experiment can be
performed with ∼ 10× higher throughput and ∼ 100× lower cost relative to 13C / 15N R1ρ and enabled
Hoogsteen chemical exchange measurements undetectable by R1ρ. The
results reveal an increased propensity to form Hoogsteen bp's near terminal
ends and a diminished propensity within A-tract motifs. The 1H CEST
experiment provides a basis for rapidly screening Hoogsteen breathing in
duplex DNA, enabling identification of unusual motifs for more in-depth
characterization.
Funder
National Institutes of Health
Publisher
Copernicus GmbH
Reference88 articles.
1. 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, https://doi.org/10.1038/s41586-020-2843-2, 2020. 2. 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. 3. 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, https://doi.org/10.1038/ncomms5786, 2014. 4. 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, https://doi.org/10.1038/s41586-020-2336-3, 2020. 5. Ben Imeddourene, A., Zargarian, L., Buckle, M., Hartmann, B., and Mauffret,
O.: Slow motions in A.T rich DNA sequence, Sci. Rep., 10, 19005, https://doi.org/10.1038/s41598-020-75645-x, 2020.
Cited by
9 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|