Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogs

Strobel, Oliver K.; Keyes, Robert S.; Bobst, Albert M.

doi:10.1021/bi00489a003

Cited by 20 publications

(26 citation statements)

References 35 publications

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“…Analysis of the EPR spectra of DUAP-labeled nucleic acids corroborates the results obtained with DUMTA-labeled DNA (Keyes and Bobst, 1995), confirming the ability to effectively monitor both local and global dynamics with spin labels of different tether length. Examination of the B-Z transition detected by DCAT-labeled polymers extends previous work (Strobel et al, 1990b), demonstrating that five-atom-tethered nitroxides are sensitive to conformational changes and associated spin-labeled base ordering. By comparing the results obtained in this laboratory of several different spin-labeled systems, a unified understanding of local and global DNA dynamics has emerged.…”

Section: Resultssupporting

confidence: 67%

“…Since the global tumbling of a polymer will be in the rigid limit, T, will not be augmented by global diffusion and will reflect the internal dynamics alone. A value of several nanoseconds for T, has consistently provided good simulations for spin-labeled B-DNA polymers in the Bobst laboratory (Kao et al, 1983; Pauly et al, 1987;Strobel et al, 1990b;Keyes and Bobst, 1995). The fact that spin labels with tethers of either two or five atoms in length reliably report nucleic acid dynamics nullifies the suggestion that these labels only monitor nitroxide motion independent of the base (Spaltenstein et al, 1989b).…”

Section: Discussionmentioning

confidence: 99%

“…Panel A illustrates the trend in Ti for six-membered ring spin labels. Values are included for 2-atom ( Keyes and Bobst, 1995), 4-atom (Bobst et al, 1984), 5-atom (Table 2), 6-atom (Bobst et al, 1984), and 11-atom (Strobel et al, 1990b) tethers. When the nitroxide is placed beyond the major groove, the value of TlI does not seem to change.…”

Section: Discussionmentioning

confidence: 99%

“…The better the coupling between the nitroxide and the base to which it is attached, the closer the nitroxide dynamics will reflect the base dynamics. Although spin labels with long tethers (i.e., 5-11 atoms in length) are not as well coupled as those with shorter tethers, they still consistently detect the magnitude of base motion (Strobel et al, 1990b(Strobel et al, , 1995. In addition, they have the advantage of being acceptable substrates for enzymatic incorporation into nucleic acids, whereas the short-tethered nitroxides (i.e., 1-2 atoms) do not incorporate well (Toppin, 1983).…”

Section: Introductionmentioning

confidence: 99%

“…When monoacetylenic tethers are used, the EPR spectra are predominantly slow-motional, and it was concluded that there is no significant -4 ns (Spaltenstein et al, 1989b) or rapid, large amplitude (Hustedt et al, 1993a(Hustedt et al, , 1995 base motion. On the other hand, evidence for substantial base dynamics has been found from crystallography (Holbrook and Kim, 1984;Klimasauskas et al, 1994), EPR (Strobel et al, 1990b(Strobel et al, , 1995, fluorescence (Nordlund et al, 1989;Guest et al, 1991;Georghiou et al, 1996), and NMR (Leroy et al, 1988;Eimer et al, 1990;Folta-Stogniew and Russu, 1994;Garcia de la Torre et al, 1994). In fact, a recent study monitoring the intrinsic fluorescence of thymine argues for the existence of large-amplitude base motions in DNA (Georghiou et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

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Overall and internal dynamics of DNA as monitored by five-atom-tethered spin labels

Keyes

Bobst

Cao

et al. 1997

Biophysical Journal

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Electron paramagnetic resonance (EPR) spectra of the two-atom-tethered six-membered ring thymidylate spin label (DUMTA) incorporated into duplexes of different sizes were found to display a helix length dependence and a local-order parameter S = 0.32 +/- 0.01 for B-DNA based on the dynamic cylinder model (Keyes, R. S., and A. M. Bobst. 1995. Detection of internal and overall dynamics of a two-atom-tethered spin-labeled DNA. Biochemistry. 34:9265-9276). This sensitivity to size, which reflects global tumbling, is now reported for the more flexible five-atom-tethered five-membered ring thymidylate spin label (DUAP) that can be readily incorporated enzymatically and sequence specifically into nucleic acids of different sizes. The DUAPs containing B-DNA systems were simulated with the same dynamic cylinder model, giving S = 0.20 +/- 0.01 for the more flexibly tethered spin label. This shows that S is dependent on tether length but not on global motion. An analysis with the same motional model of the B-Z transition in a (dG-dC)n polymer containing the five-atom-tethered six-membered ring cytidylate spin label (DCAT) (Strobel, O. K., R. S. Keyes, and A. M. Bobst. 1990b. Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogues. Biochemistry. 29:8522-8528) revealed an increase in S from 0.15 +/- 0.01 to 0.26 +/- 0.01 in response to the B- to Z-DNA transition. This indicates that S is not only sensitive to tether length, but also to conformational changes in DNA. Both the DUAP- and the DCAT-labeled systems were also simulated with a base disk model. From the DUAP spectral series, the perpendicular component of the correlation time tau perpendicular describing the spin-labeled base diffusion was found to be sensitive to global tumbling, confirming earlier results obtained with DUMTA. The DCAT polymer results demonstrated that tau perpendicular monitors a conformational change from B- to Z-DNA, indicating that tau perpendicular is also sensitive to local base dynamics. These results confirm that the dynamics of five-atom-tethered nitroxides are coupled to the nucleic acid dynamics and, as with two-atom-tethered spin labels, can be characterized by S and tau perpendicular. The analyses of both spin-labeled systems provide good evidence for spin-labeled base motions within double-stranded DNA occurring on the nanosecond time scale, and establish that both labels can be used to monitor changes in global tumbling and local order parameter due to variations in DNA conformation and protein-DNA interactions.

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Section: Resultssupporting

confidence: 67%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Overall and internal dynamics of DNA as monitored by five-atom-tethered spin labels

Keyes

Bobst

Cao

et al. 1997

Biophysical Journal

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Tandem Arrays of TEMPO and Nitronyl Nitroxide Radicals with Designed Arrangements on DNA

Atsumi¹,

Maekawa²,

Nakazawa³

et al. 2011

Chemistry A European J

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Herein we describe one-dimensional electron-spin arrays consisting of two different organic radicals with the designed arrangement based on the DNA sequence. Two mismatch-binding ligands carrying 2,2,6,6-tetramethylpiperidine N-oxide (TEMPO) and nitronyl nitroxide selectively bind to the predetermined sites on double stranded DNA. By using the two mismatch-binding ligands carrying the organic radicals as the glue for DNA, electron-spin assembly could be successfully synchronized with the hybridization. Periodically and tandemly arranged, two kinds of organic radical molecules at designed positions might be useful for an approach to build up scalable qubits of electron-spin-based quantum computing. The approach using DNA nanostructures as a scaffold to assembly functional small molecules can afford one of the promising ways for the future application of DNA nanostructures and nanotechnology.

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Site‐Directed Spin Labelling of Nucleic Acids

Shelke

Sigurdsson

2012

Eur J Org Chem

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The study of the structure and dynamics of the nucleic acids and their complexes with other biomolecules is the basis for understanding their functions. Electron paramagnetic resonance (EPR) spectroscopy is a biophysical technique that in recent years has been increasingly used to investigate nucleic acids. EPR studies require paramagnetic centre(s), usually nitroxide spin‐label(s) that are incorporated at specific sites in the nucleic acid by site‐directed spin labelling (SDSL). In the last few years, spin labels with improved spectroscopic properties have emerged and new SDSL techniques have been developed. This microreview describes SDSL of nucleic acids in the context of the three spin labelling strategies: post‐synthetic spin labelling, labelling during oligonucleotide synthesis and noncovalent labelling.

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Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogs

Cited by 20 publications

References 35 publications

Overall and internal dynamics of DNA as monitored by five-atom-tethered spin labels

Overall and internal dynamics of DNA as monitored by five-atom-tethered spin labels

Tandem Arrays of TEMPO and Nitronyl Nitroxide Radicals with Designed Arrangements on DNA

Site‐Directed Spin Labelling of Nucleic Acids

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