scholarly journals Metal-mediated base pairs in parallel-stranded DNA

2017 ◽  
Vol 13 ◽  
pp. 2671-2681 ◽  
Author(s):  
Jens Müller
Keyword(s):  
Nucleic Acid ◽  
Complex Formation ◽  
Transition Metal Ions ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Experimental Conditions ◽  
Site Specific ◽  
Glycosidic Bonds ◽  
Double Helices ◽  
Significant Extension

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

scholarly journals Symmetry in Nucleic-Acid Double Helices

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 737
Author(s):  
Udo Heinemann ◽  
Yvette Roske
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Rna Structure ◽  
Test Tube ◽  
Base Pairs ◽  
Dna And Rna ◽  
Left Handed ◽  
Double Helices ◽  
Rna Duplexes ◽  
The Right

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.

Permeability of boar and bull spermatozoa to the nucleic acid stains propidium iodide or Hoechst 33258, or to eosin: accuracy in the assessment of cell viability

Reproduction ◽  
2000 ◽  
pp. 145-152 ◽  
Author(s):  
B Pintado ◽  
J de la Fuente ◽  
ER Roldan
Keyword(s):  
Nucleic Acid ◽  
Propidium Iodide ◽  
Hoechst 33258 ◽  
Experimental Conditions ◽  
Functional Studies ◽  
Viable Cells ◽  
Direct Microscopic Examination ◽  
Acrosomal Exocytosis ◽  
Viable Sperm ◽  
Boar Spermatozoa

This study was designed to assess whether nucleic acid stains such as propidium iodide and Hoechst 33258 and the cytosolic stain eosin identified equivalent proportions of non-viable cells. Sub-samples of boar spermatozoa stored for up to 72 h, and frozen bull spermatozoa stored in straws and thawed before staining, were exposed to either propidium iodide or Hoechst 33258 alone or in combination. Additional sub-samples were stained with eosin-nigrosin and subsequently with Giemsa. The proportion of non-viable cells identified by propidium iodide alone was equivalent to that observed when it was used in combination with the other fluorescent probe. Similar results were observed for Hoechst 33258. However, direct microscopic examination of sub-samples exposed to both stains revealed that a proportion of spermatozoa stained with propidium iodide did not incorporate Hoechst 33258. This was found consistently in boar and bull spermatozoa under the different experimental conditions used. Quantification showed that the proportion of propidium iodide-positive cells was significantly higher than Hoechst 33258-positive cells. Furthermore, the proportion of propidium iodide-positive cells was higher than cells stained with eosin, but no differences were found between the number of cells stained with Hoechst 33258 or eosin. The proportion of cells stained with propidium iodide was positively correlated with the proportion stained with either Hoechst 33258 or eosin, despite the observation that more cells incorporated propidium iodide. Taken together, these results indicate that there are differences in the ability of fluorescent probes to identify non-viable sperm cells and that this should be considered when staining protocols are used to analyse sperm viability, or when viability is used as a discriminating factor in functional studies, such as those related to acrosomal exocytosis.

scholarly journals Hypochlorite and superoxide radicals can act synergistically to induce fragmentation of hyaluronan and chondroitin sulphates

2004 ◽  
Vol 381 (1) ◽  
pp. 175-184 ◽  
Author(s):  
Martin D. REES ◽  
Clare L. HAWKINS ◽  
Michael J. DAVIES
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Transition Metal Ions ◽  
Chloride Ions ◽  
Superoxide Radicals ◽  
Thermal Source ◽  
Site Specific ◽  
Trace Metal Ions ◽  
Electron Reduction ◽  
Polymer Fragmentation

Activated phagocytes release the haem enzyme MPO (myeloperoxidase) and also generate superoxide radicals (O2•−), and hence H2O2, via an oxidative burst. Reaction of MPO with H2O2 in the presence of chloride ions generates HOCl (the physiological mixture of hypochlorous acid and its anion present at pH 7.4). Exposure of glycosaminoglycans to a MPO–H2O2–Cl− system or reagent HOCl generates long-lived chloramides [R-NCl-C(O)-R′] derived from the glycosamine N-acetyl functions. Decomposition of these species by transition metal ions gives polymer-derived amidyl (nitrogen-centred) radicals [R-N•-C(O)-R′], polymer-derived carbon-centred radicals and site-specific strand scission. In the present study, we have shown that exposure of glycosaminoglycan chloramides to O2•− also promotes chloramide decomposition and glycosaminoglycan fragmentation. These processes are inhibited by superoxide dismutase, metal ion chelators and the metal ion-binding protein BSA, consistent with chloramide decomposition and polymer fragmentation occurring via O2•−-dependent one-electron reduction, possibly catalysed by trace metal ions. Polymer fragmentation induced by O2•− [generated by the superoxide thermal source 1, di-(4-carboxybenzyl)hyponitrite] was demonstrated to be entirely chloramide dependent as no fragmentation occurred with the native polymers or when the chloramides were quenched by prior treatment with methionine. EPR spin-trapping experiments using 5,5-dimethyl1-pyrroline-N-oxide and 2-methyl-2-nitrosopropane have provided evidence for both O2•− and polymer-derived carbon-centred radicals as intermediates. The results obtained are consistent with a mechanism involving one-electron reduction of the chloramides to yield polymer-derived amidyl radicals, which subsequently undergo intramolecular hydrogen atom abstraction reactions to give carbon-centred radicals. The latter undergo fragmentation reactions in a site-specific manner. This synergistic damage to glycosaminoglycans induced by HOCl and O2•− may be of significance at sites of inflammation where both oxidants are generated concurrently.

Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

2015 ◽  
Vol 39 (11) ◽  
pp. 8752-8762 ◽  
Author(s):  
Gaofeng Liu ◽  
Zhiwen Li ◽  
Junfei Zhu ◽  
Yang Liu ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Base Pairing ◽  
Dna Duplex ◽  
Base Pairs ◽  
Thermal Stabilities

Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.

Competition between Cd(II) and other divalent transition metal ions during complex formation with amino acids, peptides, and chelating agents

2016 ◽  
Vol 327-328 ◽  
pp. 55-69 ◽  
Author(s):  
Maurizio Remelli ◽  
Valeria M. Nurchi ◽  
Joanna I. Lachowicz ◽  
Serenella Medici ◽  
M. Antonietta Zoroddu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Complex Formation ◽  
Transition Metal ◽  
Metal Ions ◽  
Chelating Agents ◽  
Transition Metal Ions
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