Site-Directed Spin Labeling of DNA Reveals Mismatch-Induced Nanometer Distance Changes between Flanking Nucleotides

Wunnicke, Dorith; Ding, Ping; Seela, Frank; Steinhoff, Heinz‐Jürgen

doi:10.1021/jp212421c

Cited by 11 publications

(14 citation statements)

References 45 publications

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“…Whereas early SDSL studies used DNA duplexes as model systems (21,36,37), recent reports have emerged in which SDSL measured distances were used to study DNA duplex conformation in response to base lesion (38), mismatches (39) and protein binding (40). In addition, SDSL has also been used to study higher order DNA structures such as quadruplexes (41) and four-way junctions (42).…”

Section: Discussionmentioning

confidence: 99%

Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling

Zhang

Machado

Ding

et al. 2013

Nucleic Acids Research

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The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein–DNA interactions.

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Section: Discussionmentioning

confidence: 99%

Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling

Zhang

Machado

Ding

et al. 2013

Nucleic Acids Research

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show abstract

“…Mapping sequence-dependent DNA shape using the SDSL-MC approach Whereas early SDSL studies used DNA duplexes as model systems (21,36,37), recent reports have emerged in which SDSL measured distances were used to study DNA duplex conformation in response to base lesion (38), mismatches (39) and protein binding (40). In addition, SDSL has also been used to study higher order DNA structures such as quadruplexes (41) and four-way junctions (42).…”

Section: Sequence-dependent Conformational Changes Of Res On P53dbd Bmentioning

confidence: 99%

Conformations of P53 Response Elements in Solution Deduced using Site-Directed Spin Labeling and Monte Carlo Sampling

Zhang

Carolina

Machado

et al. 2014

Biophysical Journal

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The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electronresonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequencedependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein-DNA interactions.

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“…Because of these properties, viologen-based dendrimers were used to study electrostatic charge interactions, charge storing abilities, CT are infrequent. Several reports are available on the interspin distance measurements on oligo phenylene ethynylene molecular rods, [21,26,27] and spin-labeled biological systems such as DNA or proteins [28][29][30][31][32][33] using CW or pulsed EPR techniques. Although viologen dendrimers bearing ethyl, benzyl, and other bulky peripheral groups were reported, [9] viologen dendrimers bearing nitroxide spin labels at the periphery are not known till date.…”

Section: Introductionmentioning

confidence: 99%

TEMPO‐Labeled Viologen Dendrimers: Synthesis, Characterization, and Preliminary Distance Measurements

Kathiresan

Steinhoff

Walder

2017

Macro Chemistry & Physics

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Viologen dendrimers (G0* to G2*) bearing (2,2,6,6‐tetramethylpiperidin‐1‐yl)oxyl (TEMPO) spin labels are successfully synthesized via a divergent approach. 4‐amino TEMPO is successfully grafted onto the periphery of the dendrimer moieties using Zincke reaction under dark conditions. The final products are characterized by cyclic voltammetry and the spin‐label efficiencies are characterized by electron paramagnetic resonance (EPR) measurements. Cyclic voltammetric studies show the coexistence of both viologen as well as TEMPO electroactive subunits, and evidence for the intramolecular electrocatalytic reduction of TEMPO by viologen subunit is presented. EPR measurements show moderate to good spin‐label efficiencies (72–85%), but the spin‐labeled samples are not stable in the presence of air and light. The measured spin‐label efficiency decreases with increasing dendrimer generation. Double electron resonance measurements provide interspin distances for zeroth generation G0* dendrimers. MM+ calculations perform using Hyperchem show an averaged single spin distance (2.34 nm) for G0* dendrimers and a more complex scenario of several possible interspin distances in the case of G1* and G2* dendrimers.

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Site-Directed Spin Labeling of DNA Reveals Mismatch-Induced Nanometer Distance Changes between Flanking Nucleotides

Cited by 11 publications

References 45 publications

Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling

Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling

Conformations of P53 Response Elements in Solution Deduced using Site-Directed Spin Labeling and Monte Carlo Sampling

TEMPO‐Labeled Viologen Dendrimers: Synthesis, Characterization, and Preliminary Distance Measurements

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