Mercury Electrodes in Nucleic Acid Electrochemistry: Sensitive Analytical Tools and Probes of DNA Structure. A Review

2004 ◽  
Vol 69 (4) ◽  
pp. 715-747 ◽  
Author(s):  
Miroslav Fojta
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Double Helix ◽  
Dna Structure ◽  
Electrochemical Analysis ◽  
Label Free ◽  
Helix Formation ◽  
Mercury Electrodes ◽  
Dna Strand ◽  
Dna Double Helix

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.

scholarly journals Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy

Nanomaterials ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 326
Author(s):  
Luca Guerrini ◽  
Ramon A. Alvarez-Puebla
Keyword(s):  
Raman Spectroscopy ◽  
Nucleic Acids ◽  
Double Helix ◽  
Surface Enhanced Raman Spectroscopy ◽  
Label Free ◽  
Helix Formation ◽  
Phosphate Backbone ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Triplex Structure

Direct, label-free analysis of nucleic acids via surface-enhanced Raman spectroscopy (SERS) has been continuously expanding its range of applications as an intriguing and powerful analytical tool for the structural characterization of diverse DNA structures. Still, interrogation of nucleic acid tertiary structures beyond the canonical double helix often remains challenging. In this work, we report for the first time the structural identification of DNA triplex structures. This class of nucleic acids has been attracting great interest because of their intriguing biological functions and pharmacological potential in gene therapy, and the ability for precisely engineering DNA-based functional nanomaterials. Herein, structural discrimination of the triplex structure against its duplex and tertiary strand counterparts is univocally revealed by recognizing key markers bands in the intrinsic SERS fingerprint. These vibrational features are informative of the base stacking, Hoogsteen hydrogen bonding and sugar–phosphate backbone reorganization associated with the triple helix formation. This work expands the applicability of direct SERS to nucleic acids analysis, with potential impact on fields such as sensing, biology and drug design.

scholarly journals Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Masayuki Fujii ◽  
Naoki Sugimoto
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Double Helix ◽  
Nucleoside Analogs ◽  
Structural Analog ◽  
Base Pairs ◽  
Nucleic Acid Analogs ◽  
Dna Double Helix ◽  
Nucleic Acid Interactions ◽  
Site Selective

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

CHIASMUS IN ART AND TEXT

2013 ◽  
Vol 60 (1) ◽  
pp. 50-88
Author(s):  
Edmund Thomas
Keyword(s):  
Molecular Structure ◽  
Twentieth Century ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Double Helix ◽  
Scientific Article ◽  
Deoxyribose Nucleic Acid ◽  
Francis Crick

Sixty years ago, on 25 April 1953, probably the most influential scientific article of the twentieth century appeared. Its uninviting title, ‘Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid’, concealed the revolutionary discovery by the molecular biologists James Watson and Francis Crick of the structure of what became known as ‘the molecule of life’. The ‘radically different structure’ that they proposed for the salt of deoxyribose nucleic acid (DNA) had ‘two helical chains each coiled round the same axis’. ‘Both chains’, they wrote, ‘follow right-handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite directions.’ When Bruno J. Strasser asked in the same journal fifty years later ‘Who cares about the double helix?’, he answered that it marked ‘an age of (lost) innocence, when youth, intelligence and self-assurance were sufficient to make great discoveries in science’.

Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA

2015 ◽  
Vol 13 (8) ◽  
pp. 2366-2374 ◽  
Author(s):  
Vipin Kumar ◽  
Venkitasamy Kesavan ◽  
Kurt V. Gothelf
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Triple Helix ◽  
Helical Structures ◽  
Single Stranded Dna ◽  
Dna And Rna ◽  
Helix Formation ◽  
Triple Helix Formation

Homopyrimidine acyclic (l)-threoninol nucleic acid (aTNA) was synthesized and found to form highly stable (l)-aTNA–DNA–(l)-aTNA and (l)-aTNA–RNA–(l)-aTNA triple helical structures.

scholarly journals Label-free horizontal EMSA for analysis of protein-RNA interactions

2019 ◽  
Author(s):  
William Perea ◽  
Nancy L. Greenbaum
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Dissociation Constant ◽  
Intermolecular Interactions ◽  
Ethidium Bromide ◽  
Fluorescent Labeling ◽  
Label Free ◽  
Cationic Protein ◽  
Intercalating Dye ◽  
Protein Components

AbstractWe describe a method to analyze the affinity and specificity of interactions between proteins and RNA using horizontal PAGE under non-denaturing conditions. The method permits tracking of migration of anionic and cationic biomolecules and complexes toward anode and cathode, respectively, therefore enabling quantification of bound and free biomolecules of different charges and affinity of their intermolecular interactions. The gel is stained with a fluorescent intercalating dye (SYBR®Gold or ethidium bromide) for visualization of nucleic acids followed by Coomassie® Brilliant Blue R-250 for visualizations of proteins; the dissociation constant is determined separately from the intensity of unshifted and shifted bands visualized by each dye. The method permits calculation of bound and unbound anionic nucleic acid and cationic protein components in the same gel, regardless of charge, under identical conditions, and avoids the need for radioisotope or fluorescent labeling of either component.

scholarly journals Mechanism of RPA-Facilitated Processive DNA Unwinding by the Eukaryotic CMG Helicase

2019 ◽  
Author(s):  
Hazal B. Kose ◽  
Sherry Xie ◽  
George Cameron ◽  
Melania S. Strycharska ◽  
Hasan Yardimci
Keyword(s):  
Single Molecule ◽  
Replication Fork ◽  
Double Helix ◽  
Dna Unwinding ◽  
Helicase Activity ◽  
Replicative Helicase ◽  
Double Stranded Dna ◽  
Order Of Magnitude ◽  
Dna Strand ◽  
Dna Double Helix

AbstractThe DNA double helix is unwound by the Cdc45/Mcm2-7/GINS (CMG) complex at the eukaryotic replication fork. While isolated CMG unwinds duplex DNA very slowly, its fork unwinding rate is stimulated by an order of magnitude by single-stranded DNA binding protein, RPA. However, the molecular mechanism by which RPA enhances CMG helicase activity remained elusive. Here, we demonstrate that engagement of CMG with parental double-stranded DNA (dsDNA) at the replication fork impairs its helicase activity, explaining the slow DNA unwinding by isolated CMG. Using single-molecule and ensemble biochemistry, we show that binding of RPA to the excluded DNA strand prevents duplex engagement by the helicase and speeds up CMG-mediated DNA unwinding. When stalled due to dsDNA interaction, DNA rezipping-induced helicase backtracking re-establishes productive helicase-fork engagement underscoring the significance of plasticity in helicase action. Together, our results elucidate the dynamics of CMG at the replication fork and reveal how other replisome components can mediate proper DNA engagement by the replicative helicase to achieve efficient fork progression.

scholarly journals Spontaneous Assembly of an Organic-Inorganic Nucleic Acid Z-DNA Double-Helix Structure

2016 ◽  
Vol 56 (4) ◽  
pp. 1141-1145 ◽  
Author(s):  
Vladislav Kulikov ◽  
Naomi A. B. Johnson ◽  
Andrew J. Surman ◽  
Marie Hutin ◽  
Sharon M. Kelly ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Double Helix ◽  
Helix Structure ◽  
Z Dna ◽  
Double Helix Structure ◽  
Dna Double Helix

Nanostructure-based surface-enhanced Raman scattering biosensors for nucleic acids and proteins

2016 ◽  
Vol 4 (10) ◽  
pp. 1757-1769 ◽  
Author(s):  
Jie Chao ◽  
Wenfang Cao ◽  
Shao Su ◽  
Lixing Weng ◽  
Shiping Song ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Raman Scattering ◽  
Nucleic Acids ◽  
Protein Detection ◽  
Surface Enhanced Raman Scattering ◽  
Label Free ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering

Nanostructure-based SERS platforms have been developed for nucleic acid and protein detection ranging from label-free, labeled and multiplex analyses.

Structure of DNA and Nucleosome Observed by Ultrahigh-Resolution SEM

1990 ◽  
Vol 48 (3) ◽  
pp. 124-125
Author(s):  
Sumire Inaga ◽  
Hitoshi Osatake ◽  
Akihiro lino ◽  
Keiichi Tanaka
Keyword(s):  
Electron Microscopy ◽  
Double Helix ◽  
Replica Method ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Ultrahigh Resolution ◽  
Naked Dna ◽  
Dna Strands ◽  
Dna Strand ◽  
Dna Double Helix

So far, the ultrastructure of DNA strand and nucleosome had been observed mainly by transmission electron microscopy with some techniques (thin-sectioning, spreading method, replica method and so on). Among them, the freeze-etching replica method gave high magnified images of DNA double helix (Ruben et al., 1989). Further, scanning tunneling microscopy also elucidated the images of major and minor grooves in a helical DNA duplex. Though scanning electron microscopy (SEM) was also applied for observing chromatin structures, it had been difficult to observe clearly such small materials. Because, the resolution of SEM was too poor to investigate such fine structures. The obstruction of resolution, however, was overcome by the development of an ultrahigh resolution SEM (UHS-T1, Tanaka et al., 1985). Using the SEM, we could successfully observed naked DNA strands and nucleosomes of chicken erythrocyte nuclei without any metal-coating.Preparations were made by the microspreading procedure basically according to the method of Seki et al.

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