Determination of Redox Potentials for the Watson−Crick Base Pairs, DNA Nucleosides, and Relevant Nucleoside Analogues

2007 ◽  
Vol 111 (19) ◽  
pp. 5386-5395 ◽  
Author(s):  
Carlos E. Crespo-Hernández ◽  
David M. Close ◽  
Leonid Gorb ◽  
Jerzy Leszczynski
Keyword(s):  
Nucleoside Analogues ◽  
Redox Potentials ◽  
Base Pairs

Quantitative determination of the number of secondary and tertiary structure base pairs in transfer RNA in solution

Biochemistry ◽  
1976 ◽  
Vol 15 (20) ◽  
pp. 4370-4377 ◽  
Author(s):  
P. H. Bolton ◽  
C. R. Jones ◽  
D. Bastedo-Lerner ◽  
K. L. Wong ◽  
D. R. Kearns
Keyword(s):  
Quantitative Determination ◽  
Tertiary Structure ◽  
Transfer Rna ◽  
Base Pairs ◽  
Secondary And Tertiary Structure

scholarly journals Accurate geometrical restraints for Watson–Crick base pairs

2019 ◽  
Vol 75 (2) ◽  
pp. 235-245 ◽  
Author(s):  
Miroslaw Gilski ◽  
Jianbo Zhao ◽  
Marcin Kowiel ◽  
Dariusz Brzezinski ◽  
Douglas H. Turner ◽  
...  
Keyword(s):  
Structural Information ◽  
Data Bank ◽  
Base Pairs ◽  
Acta Cryst ◽  
Ultrahigh Resolution ◽  
Cryo Electron Microscopy ◽  
Structural Database ◽  
Different Sources ◽  
Best Parameters

Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.

scholarly journals XANES-Based Determination of Redox Potentials Imposed by Steel Corrosion Products in Cement-Based Media

2018 ◽  
Author(s):  
Bin Ma ◽  
Alejandro Fernandez-Martinez ◽  
Benoît Madé ◽  
Nathaniel Findling ◽  
Ekaterina Markelova ◽  
...  
Keyword(s):  
Steel Corrosion ◽  
Corrosion Products ◽  
Redox Potentials

scholarly journals Fluorescent Method for the Detection of Biothiols Using an Ag+-Mediated Conformational Switch

Sensors ◽  
2019 ◽  
Vol 19 (4) ◽  
pp. 934 ◽  
Author(s):  
Han Zhao ◽  
Mingjian Chen ◽  
Changbei Ma
Keyword(s):  
Clinical Practice ◽  
Dna Probe ◽  
Fluorescence Signal ◽  
Base Pairs ◽  
Time Saving ◽  
Conformational Switch ◽  
Fluorescent Method ◽  
High Fluorescence Intensity ◽  
High Fluorescence

In this work, a novel, simple, and time-saving fluorescence approach for the detection of biothiols (glutathione and cysteine) was developed by employing a DNA probe labeled with 2-aminopurine. As an adenine analogue, 2-aminopurine exhibits high fluorescence intensity that can be rapidly quenched in the presence of DNA. In the presence of Ag+, the fluorescence increased significantly, which was a result of the formation of cytosine–Ag+–cytosine base pairs and the release of 2-aminopurine. Upon addition of either glutathione or cysteine, the structure of cytosine–Ag+–cytosine was disrupted, a product of the stronger affinity between biothiols and Ag+. As a result, the 2-aminopurine-labeled DNA probe returned to its former structure, and the fluorescence signal was quenched accordingly. The detection limit for glutathione and cysteine was 3 nM and 5 nM, respectively. Furthermore, the determination of biothiols in human blood serum provided a potential application for the probe as a diagnostic tool in clinical practice.

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