Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reversible DNA i-motif to hairpin switching induced by copper(II) cations.

ABSTRACT: i-Motif DNA structures have previously been utilised for many different nanotechnological applications, but all have used changes in pH to fold the DNA. Herein we describe how copper(II) cations can alter the conformation of i-motif DNA into an alternative hairpin structure which is reversible by chelation with EDTA.

SUBMITTER: Day HA

PROVIDER: S-EPMC4563791 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Reversible DNA i-motif to hairpin switching induced by copper(II) cations.

Day Henry Albert HA Wright Elisé Patricia EP MacDonald Colin John CJ Gates Andrew James AJ Waller Zoë Ann Ella ZA

Chemical communications (Cambridge, England) 20150901 74

i-Motif DNA structures have previously been utilised for many different nanotechnological applications, but all have used changes in pH to fold the DNA. Herein we describe how copper(II) cations can alter the conformation of i-motif DNA into an alternative hairpin structure which is reversible by chelation with EDTA. ...[more]

PMID: 26252811

Similar Datasets

Redox-dependent control of i-Motif DNA structure using copper cations.

Project description:Previous computational studies have shown that Cu+ can act as a substitute for H+ to support formation of cytosine (C) dimers with similar conformation to the hemi-protonated base pair found in i-motif DNA. Through a range of biophysical methods, we provide experimental evidence to support the hypothesis that Cu+ can mediate C-C base pairing in i-motif DNA and preserve i-motif structure. These effects can be reversed using a metal chelator, or exposure to ambient oxygen in the air that drives oxidation of Cu+ to Cu2+, a comparatively weak ligand. Herein, we present a dynamic and redox-sensitive system for conformational control of an i-motif forming DNA sequence in response to copper cations.

| S-EPMC6159522 | biostudies-literature

Reversible energy-transfer switching on a DNA scaffold.

Project description:We show that FRET between Pacific Blue (PB) and Alexa488 (A488) covalently attached to a DNA scaffold can be reversibly controlled by photochromic switching of a spiropyran derivative. With the spiropyran in the closed spiro isomeric form, FRET occurs freely between PB and A488. UV-induced isomerization to the open merocyanine form shuts down the FRET process by efficient quenching of the PB excited state. The process is reversed by exposure to visible light, triggering the isomerization to the spiro isomer.

| S-EPMC4353014 | biostudies-literature

Reversible structural switching of a DNA-DDAB film.

Project description:We describe the novel structure and behavior of a DNA-DDAB complex film cast from an organic solvent and exhibiting a structural switching transition as it is dried or wetted with water. The film was easily prepared by formation of a complex between the negatively charged phosphate groups of DNA and the positively charged headgroup of the surfactant DDAB. This complex was then purified, dried, dissolved in 2-propanol, and cast onto a glass slide to form a self-standing film by means of slow evaporation. While the structure of the dried film was found to be composed of single-stranded DNA and a monolayer of DDAB, upon hydration of the film, the structure switched to double-stranded DNA complexed to a bilayer of DDAB. We expect this phenomenon to serve as a useful model for the design of new responsive materials and programmable self-assembly.

| S-EPMC2664520 | biostudies-literature

Tuning transport in graphene oxide membrane with single-site copper (II) cations.

Project description:Controlling the ion transport through graphene oxide (GO) membrane is challenging, particularly in the aqueous environment due to its strong swelling tendency. Fine-tuning the interlayer spacing and chemistry is critical to create highly selective membranes. We investigate the effect of single-site divalent cations in tuning GO membrane properties. Competitive ionic permeation test indicates that Cu2+ cations dominate the transport through the 2D channels of GO membrane over other cations (Mg2+/Ca2+/Co2+). Without/With the single-site M2+ modifications, pristine GO, Mg-GO, Ca-GO, and Cu-GO membranes show interlayer spacings of ∼13.6, 15.6, 14.5, and 12.3 Å in wet state, respectively. The Cu-GO membrane shows a two-fold decrease of NaCl (1 M) permeation rate comparing to pristine GO, Mg-GO, and Ca-GO membranes. In reverse osmosis tests using 1000 ppm NaCl and Na2SO4 as feeds, Cu-GO membrane shows rejection of ∼78% and ∼94%, respectively, which are 5%-10% higher than its counterpart membranes.

| S-EPMC8961230 | biostudies-literature

Mechanotransduction-Induced Reversible Phenotypic Switching in Prostate Cancer Cells.

Project description:Phenotypic plasticity is posed to be a vital trait of cancer cells such as circulating tumor cells, allowing them to undergo reversible or irreversible switching between phenotypic states important for tumorigenesis and metastasis. While irreversible phenotypic switching can be detected by studying the genome, reversible phenotypic switching is often difficult to examine due to its dynamic nature and the lack of knowledge about its contributing factors. In this study, we demonstrate that culturing cells in different physical environments, stiff, soft, or suspension, induced a phenotypic switch in prostate cancer cells via mechanotransduction. The mechanosensitive phenotypic switching in prostate cancer cells was sustainable yet reversible even after long-term culture, demonstrating the impact of mechanical signals on prostate cancer cell phenotypes. Importantly, such a mechanotransduction-mediated phenotypic switch in prostate cancer cells was accompanied by decreased sensitivity of the cells to paclitaxel, suggesting a role of mechanotransduction in the evolution of drug resistance. Multiple signaling pathways such as p38MAPK, ERK, and Wnt were found to be involved in the mechanotransduction-induced phenotypic switching of prostate cancer cells. Given that cancer cells experience different physical environments during disease progression, this study provides useful information about the important role of mechanotransduction in cancer, and how circulating tumor cells may be capable of continuously changing their phenotypes throughout the disease process.

| S-EPMC5376107 | biostudies-literature

Two cyclometalated Pt(ii) complexes showing reversible phosphorescence switching due to grinding-induced destruction and crystallization-induced formation of supramolecular dimer structure.

Project description:Complexes [Pt(dfppy)(pbdtmi)]PF6 (1) and [Pt(ppy)(pbdtmi)]PF6 (2) have been constructed based on dithienylethene-based N^N ligand pbdtmi, showing supramolecular dimer structure in which two coordination cations connect each other through π⋯π stacking interaction. The crystalline state samples of both 1 and 2 reveal strong phosphorescence (emission peak: around 579 nm for 1, and 551 nm for 2). Interestingly, a grinding treatment for either 1 or 2 leads to phosphorescence switching from on-state to off-state. The subsequent crystallization with toluene recovers the initial on-state. This work discusses the relationship between the supramolecular dimer structures and the related phosphorescence switching behaviors in 1 and 2, and also explores the photochromism of pbdtmi, 1 and 2.

| S-EPMC8978655 | biostudies-literature

Electrochemical gating-induced reversible and drastic resistance switching in VO2 nanowires.

Project description:Reversible and drastic modulation of the transport properties in vanadium dioxide (VO2) nanowires by electric field-induced hydrogenation at room temperature was demonstrated using the nanogaps separated by humid air in field-effect transistors with planer-type gates (PG-FET). These PG-FETs allowed us to investigate behavior of revealed hydrogen intercalation and diffusion aspects with time and spatial evolutions in nanowires. These results show that air nanogaps can operate as an electrochemical reaction field, even in a gaseous atmosphere, and offer new directions to explore emerging functions for electronic and energy devices in oxides.

| S-EPMC4653652 | biostudies-literature

Stimuli Responsive Silylene: Electromerism Induced Reversible Switching Between Mono- and Bis-Silylene.

Project description:Electromerism is a very well-known phenomenon in transition metal chemistry. In main group chemistry, this concept has only started getting attention recently. We report stimuli responsive low-valent silicon compounds exhibiting electromerism. A mixed-valent silaiminyl-silylene 1, [LSi-Si(NDipp)L] (L=PhC(Nt Bu)2 ), was synthesized in a single step from amidinate-chlorosilylene. Compound 1 has two interconnected Si atoms in formally +I and +III oxidation states. Upon treatment with Lewis acidic CuI X (X=mesityl, Cl, Br, I), electron redistribution occurs resulting in the formation of [{LSi(NDipp)Si(L)}-CuX], in which both silicon atoms are in the +II formal oxidation state. Removal of the copper center from [{LSi(NDipp)Si(L)}-CuX] by using a Lewis basic carbene led to reformation of the precursor [LSi-Si(NDipp)L]. Thus, the process is fully reversible. This showcases the first example of Lewis acid/base-induced reversible electromerism in silicon chemistry.

| S-EPMC9828679 | biostudies-literature

Optically Induced Ferroelectric Polarization Switching in a Molecular Ferroelectric with Reversible Photoisomerization.

Project description:Ferroelectrics usually exhibit temperature-triggered structural changes, which play crucial roles in controlling their physical properties. However, although light is very striking as a non-contact, non-destructive, and remotely controlled external stimuli, ferroelectric crystals with light-triggered structural changes are very rare, which holds promise for optical control of ferroelectric properties. Here, an organic molecular ferroelectric, N-salicylidene-2,3,4,5,6-pentafluoroaniline (SA-PFA), which shows light-triggered structural change of reversible photoisomerization between cis-enol and trans-keto configuration is reported. SA-PFA presents clear ferroelectricity with the saturate polarization of 0.84 μC cm-2 , larger than those of some typical organic ferroelectrics with thermodynamically structural changes. Benefit from the reversible photoisomerization, the dielectric real part of SA-PFA can be reversibly switched by light. More strikingly, the photoisomerization enables SA-PFA to show reversible optically induced ferroelectric polarization switching. Such intriguing behaviors make SPFA a potential candidate for application in next-generation photo-controlled ferroelectric devices. This work sheds light on further exploration of more excellent molecular ferroelectrics with light-triggered structural changes for optical control of ferroelectric properties.

| S-EPMC8693059 | biostudies-literature

Biochemical Characterization of Kat1: a Domesticated hAT-Transposase that Induces DNA Hairpin Formation and MAT-Switching.

Project description:Kluyveromyces lactis hAT-transposase 1 (Kat1) generates hairpin-capped DNA double strand breaks leading to MAT-switching (MATa to MATα). Using purified Kat1, we demonstrate the importance of terminal inverted repeats and subterminal repeats for its endonuclease activity. Kat1 promoted joining of the transposon end into a target DNA molecule in vitro, a biochemical feature that ties Kat1 to transposases. Gas-phase Electrophoretic Mobility Macromolecule analysis revealed that Kat1 can form hexamers when complexed with DNA. Kat1 point mutants were generated in conserved positions to explore structure-function relationships. Mutants of predicted catalytic residues abolished both DNA cleavage and strand-transfer. Interestingly, W576A predicted to be impaired for hairpin formation, was active for DNA cleavage and supported wild type levels of mating-type switching. In contrast, the conserved CXXH motif was critical for hairpin formation because Kat1 C402A/H405A completely blocked hairpinning and switching, but still generated nicks in the DNA. Mutations in the BED zinc-finger domain (C130A/C133A) resulted in an unspecific nuclease activity, presumably due to nonspecific DNA interaction. Kat1 mutants that were defective for cleavage in vitro were also defective for mating-type switching. Collectively, this study reveals Kat1 sharing extensive biochemical similarities with cut and paste transposons despite being domesticated and evolutionary diverged from active transposons.

| S-EPMC4763223 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data