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Detecting the DNA kinks in a DNA–CRP complex in solution with iodine-125 radioprobing

Nature Structural Biology volume 6, pages 747–750 (1999)Cite this article

Abstract

Auger-electron-emitting radioisotopes such as 125I produce DNA strand breaks within nanometer range of the decay site. Here we analyze these breaks in order to study changes in DNA conformation upon binding with cyclic AMP receptor protein (CRP) in solution. The clear difference we found in break frequency in the CRP–DNA complex, as compared to the naked DNA duplex, correlates with the increased distances between the deoxyriboses and the radioiodine atom caused by the CRP-induced kink observed in the cocrystal. Thus, we demonstrate that 125I radioprobing can be used to study fine conformational changes of DNA within DNA–protein complexes.

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Figure 1: CRP-induced DNA kink and the 125I-sugar distances.
Figure 2: Sequence and labeling schemes of DNA duplex.
Figure 3: CRP binding to DNA.
Figure 4: Analysis of 125I-induced DNA strand breaks in 20% denaturing PAGE.
Figure 5: Frequencies of breaks in individual nucleotides (a,b) and the distances from the deoxyriboses to the 125I atom (c,d) calculated from the crystal structures16,22.

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Authors and Affiliations

  1. Nuclear Medicine Department, National Institutes of Health, Bethesda, 20892-1180, Maryland, USA

    Valeri N. Karamychev, Ronald D. Neumann & Igor G. Panyutin

  2. Novosibirsk Institute of Bioorganic Chemistry, Novosibirsk, 630090, Russia

    Valeri N. Karamychev

  3. National Cancer Institute, National Institutes of Health, Bethesda, 20892-1180, Maryland, USA

    Victor B. Zhurkin & Susan Garges

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  1. Valeri N. Karamychev
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Correspondence to Igor G. Panyutin.

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Karamychev, V., Zhurkin, V., Garges, S. et al. Detecting the DNA kinks in a DNA–CRP complex in solution with iodine-125 radioprobing. Nat Struct Mol Biol 6, 747–750 (1999). https://doi.org/10.1038/11519

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