scholarly journals Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç

2011 ◽  
Vol 40 (8) ◽  
pp. 3732-3740 ◽  
Author(s):  
Sandip A. Shelke ◽  
Snorri Th. Sigurdsson
Biochemistry ◽  
1997 ◽  
Vol 36 (39) ◽  
pp. 11629-11639 ◽  
Author(s):  
Ke Yu Wang ◽  
Sharon A. Parker ◽  
Igor Goljer ◽  
Philip H. Bolton

2019 ◽  
Vol 48 (2) ◽  
pp. 924-933 ◽  
Author(s):  
Marcel Heinz ◽  
Nicole Erlenbach ◽  
Lukas S Stelzl ◽  
Grace Thierolf ◽  
Nilesh R Kamble ◽  
...  

Abstract Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.


ChemBioChem ◽  
2012 ◽  
Vol 13 (5) ◽  
pp. 684-690 ◽  
Author(s):  
Sandip A. Shelke ◽  
Snorri Th. Sigurdsson
Keyword(s):  

Biochemistry ◽  
1992 ◽  
Vol 31 (46) ◽  
pp. 11614-11619 ◽  
Author(s):  
Igor Goljer ◽  
Jane M. Withka ◽  
Jung Yie Kao ◽  
Philip H. Bolton

1992 ◽  
Vol 20 (18) ◽  
pp. 4761-4764 ◽  
Author(s):  
Naoko Hori ◽  
Tomoko Doi ◽  
Yoko Karaki ◽  
Masakazu Kituchi ◽  
Morio Ikehara ◽  
...  

2008 ◽  
Vol 22 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Danuta Pentak ◽  
Wiesław W. Sułkowski ◽  
Agnieszka Wolińska ◽  
Sławomir Maślanka ◽  
Barbara Bojko ◽  
...  

The EPR spectroscopy was used to determine the structure and physicochemical properties of liposomes prepared from L-α-phosphatidylcholine dipalmitoyl (DPPC) by the modified reverse-phase evaporation method (mREV). EPR study was carried out in the temperature range from 297 K to 340 K i.e. below and above the phase transition temperatureTCof DPPC. On the basis of EPR spectra of spin marker 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) incorporated into the liposome, the parameterfwas determined. TEMPO dissolves easily in water and in the fluid lamellar smectic liquid-crystaline phase of lipid bilayer but is largely excluded from the solid, gel-phase. Thus TEMPO can be used to observe the change in the partition between aqueous and fluid lipid regions. The change in the relative value offas a function of temperature for DPPC shows that, in the presence of water excess, this phospholipids undergoes a transition from a “gel phase” to a lamellar smectic liquid crystalline phase. On the basis of EPR spectra of spin marker 2-(3carboxypropyl)-4,4-dimethyl-2-tridecyl-3-oxazolidinloxyl (5-DOXYL) incorporated into liposome, the parametera'Nwas determined. The isotropic14N-hyperfine coupling constanta'Nof nitroxide spin label depends on the local environmental polarity. The increase ofa'Nvalue reflects the rise of polarity of spin label environment. Temperature, cholesterol and pH dependent structural changes were also described.


1995 ◽  
Vol 90 (2) ◽  
pp. 133-138 ◽  
Author(s):  
Dwight M. Peterson ◽  
Jed Fisher ◽  
Howard D. Beall ◽  
David Ross

2017 ◽  
Vol 15 (39) ◽  
pp. 8341-8353 ◽  
Author(s):  
Aaron M. Fleming ◽  
Cynthia J. Burrows

8-Oxo-2′-deoxyguanosine in a tandem lesion context is two orders of magnitude more susceptible to oxidation than in a context of native DNA yielding hydantoin products.


2019 ◽  
Vol 316 (5) ◽  
pp. C722-C730
Author(s):  
Laura Galazzo ◽  
Leonardo Nogara ◽  
Francesca LoVerso ◽  
Antonino Polimeno ◽  
Bert Blaauw ◽  
...  

Electron paramagnetic resonance (EPR), coupled with site-directed spin labeling, has been proven to be a particularly suitable technique to extract information on the fraction of myosin heads strongly bound to actin upon muscle contraction. The approach can be used to investigate possible structural changes occurring in myosin of fiber s altered by diseases and aging. In this work, we labeled myosin at position Cys707, located in the SH1-SH2 helix in the myosin head cleft, with iodoacetamide spin label, a spin label that is sensitive to the reorientational motion of this protein during the ATPase cycle and characterized the biochemical states of the labeled myosin head by means of continuous wave EPR. After checking the sensitivity and the power of the technique on different muscles and species, we investigated whether changes in the fraction of strongly bound myosin heads might explain the contractile alterations observed in atrophic and hypertrophic murine muscles. In both conditions, the difference in contractile force could not be justified simply by the difference in muscle mass. Our results showed that in atrophic muscles the decrease in force generation was attributable to a lower fraction of strongly bound cross bridges during maximal activation. In contrast in hypertrophic muscles, the increase in force generation was likely due to several factors, as pointed out by the comparison of the EPR experiments with the tension measurements on single skinned fibers.


2013 ◽  
Vol 135 (3) ◽  
pp. 1015-1025 ◽  
Author(s):  
Kevin M. Johnson ◽  
Nathan E. Price ◽  
Jin Wang ◽  
Mostafa I. Fekry ◽  
Sanjay Dutta ◽  
...  

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