Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Helix-Dependent Spin Filtering through the DNA Duplex.

ABSTRACT: Recent work suggests that electrons can travel through DNA and other chiral molecules in a spin-selective manner, but little is known about the origin of this spin selectivity. Here we describe experiments on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. Our results show that the two spins migrate through duplex DNA with a different yield and that spin selectivity requires charge transport through the DNA duplex. Significantly, shifting the same duplex DNA between right-handed B- and left-handed Z-forms leads to a diode-like switch in spin selectivity; which spin moves more efficiently through the duplex depends upon the DNA helicity. With DNA, the supramolecular organization of chiral moieties, rather than the chirality of the individual monomers, determines the selectivity in spin, and thus a conformational change can switch the spin selectivity.

SUBMITTER: Zwang TJ

PROVIDER: S-EPMC5175457 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Helix-Dependent Spin Filtering through the DNA Duplex.

Zwang Theodore J TJ Hürlimann Sylvia S Hill Michael G MG Barton Jacqueline K JK

Journal of the American Chemical Society 20161122 48

Recent work suggests that electrons can travel through DNA and other chiral molecules in a spin-selective manner, but little is known about the origin of this spin selectivity. Here we describe experiments on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. Our results show that the two spins migrate through duplex DNA with a different yield and that spin selectivity requires charge transport through the DNA duplex. Significantly, shift ...[more]

PMID: 27934017

Similar Datasets

Spin Filtering Along Chiral Polymers.

Project description:Spin-dependent conduction and polarization in chiral polymers were studied for polymers organized as self-assembled monolayers with conduction along the polymer backbone, namely, along its longer axis. Large spin polarization and magnetoresistance effects were observed, showing a clear dependence on the secondary structure of the polymer. The results indicate that the spin polarization process does not include spin flipping and hence it results from backscattering probabilities for the two spin states.

| S-EPMC7496609 | biostudies-literature

Light-controlled spin filtering in bacteriorhodopsin.

Project description:The role of the electron spin in chemistry and biology has received much attention recently owing to to the possible electromagnetic field effects on living organisms and the prospect of using molecules in the emerging field of spintronics. Recently the chiral-induced spin selectivity effect was observed by electron transmission through organic molecules. In the present study, we demonstrated the ability to control the spin filtering of electrons by light transmitted through purple membranes containing bacteriorhodopsin (bR) and its D96N mutant. The spin-dependent electrochemical cyclic voltammetry (CV) and chronoamperometric measurements were performed with the membranes deposited on nickel substrates. High spin-dependent electron transmission through the membranes was observed; however, after the samples were illuminated by 532 nm light, the spin filtering in the D96N mutant was dramatically reduced whereas the light did not have any effect on the wild-type bR. Beyond demonstrating spin-dependent electron transmission, this work also provides an interesting insight into the relationship between the structure of proteins and spin filtering by conducting electrons.

| S-EPMC4330096 | biostudies-literature

Spin-dependent recombination probed through the dielectric polarizability.

Project description:Despite residing in an energetically and structurally disordered landscape, the spin degree of freedom remains a robust quantity in organic semiconductor materials due to the weak coupling of spin and orbital states. This enforces spin-selectivity in recombination processes which plays a crucial role in optoelectronic devices, for example, in the spin-dependent recombination of weakly bound electron-hole pairs, or charge-transfer states, which form in a photovoltaic blend. Here, we implement a detection scheme to probe the spin-selective recombination of these states through changes in their dielectric polarizability under magnetic resonance. Using this technique, we access a regime in which the usual mixing of spin-singlet and spin-triplet states due to hyperfine fields is suppressed by microwave driving. We present a quantitative model for this behaviour which allows us to estimate the spin-dependent recombination rate, and draw parallels with the Majorana-Brossel resonances observed in atomic physics experiments.

| S-EPMC4600752 | biostudies-literature

Exploring potentially alternative non-canonical DNA duplex structures through simulation.

Project description:Hopkins proposed an alternative and chirally distinct family of double-stranded DNA (dsDNA) models that have antiparallel chains with 5'→3' senses opposite to those of the right-handed Watson-Crick (WC) family. Termed configuration II, this family of dsDNA models contains both right-handed (II-R) and left-handed (II-L) forms, with Z-DNA as an example of the latter. Relative interstrand binding energies for six DNA duplex models, two each of configuration I-R (standard WC canonical B-DNA), II-R, and II-L for the duplex d(CGCGAATTCGCG), have been estimated under identical conditions using MM-PBSA analysis from molecular dynamics trajectories using three different AMBER force fields. These simulations support the stereo chemical soundness of configuration II dsDNA forms. Recent force fields (Barcelona Supercomputing Center [BSC] [bsc1] and Olomouc 2015 [OL15]) successfully render stable II-L structures, whereas the previous force field, bsc0, generated stable II-R structures, although with an energy difference between II-R and II-L of ∼30 kcal/mol. Communicated by Ramaswamy H. Sarma.

| S-EPMC7508566 | biostudies-literature

Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold.

Project description:Agrobacterium tumefaciens VirC2 stimulates processing of single-stranded T-DNA that is translocated into plants to induce tumor formation, but how VirC2 functions is unclear. Here, we report the 1.7-A X-ray crystal structure of its trypsin-resistant C-terminal domain, VirC2(82-202), which reveals a form of the ribbon-helix-helix (RHH) DNA-binding fold contained within a single polypeptide chain. DNA-binding assays and mutagenesis indicate that VirC2 uses this RHH fold to bind double-stranded DNA but not single-stranded DNA. Mutations that severely affect VirC2 DNA binding are highly deleterious for both T-DNA transfer into yeast and the virulence of A. tumefaciens in different plants including Nicotiana glauca and Kalanchoe daigremontiana. These data suggest that VirC2 enhances T-DNA transfer and virulence through DNA binding with its RHH fold. The RHH fold of VirC2 is the first crystal structure representing a group of predicted RHH proteins that facilitate endonucleolytic processing of DNA for horizontal gene transfer.

| S-EPMC2700979 | biostudies-literature

Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences.

Project description:G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions.

| S-EPMC3753619 | biostudies-literature

DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif.

Project description:The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.

| S-EPMC4737164 | biostudies-literature

Inversion of Spin Signal and Spin Filtering in Ferromagnet|Hexagonal Boron Nitride-Graphene van der Waals Heterostructures.

Project description:Two dimensional atomically thin crystals of graphene and its insulating isomorph hexagonal boron nitride (h-BN) are promising materials for spintronic applications. While graphene is an ideal medium for long distance spin transport, h-BN is an insulating tunnel barrier that has potential for efficient spin polarized tunneling from ferromagnets. Here, we demonstrate the spin filtering effect in cobalt|few layer h-BN|graphene junctions leading to a large negative spin polarization in graphene at room temperature. Through nonlocal pure spin transport and Hanle precession measurements performed on devices with different interface barrier conditions, we associate the negative spin polarization with high resistance few layer h-BN|ferromagnet contacts. Detailed bias and gate dependent measurements reinforce the robustness of the effect in our devices. These spintronic effects in two-dimensional van der Waals heterostructures hold promise for future spin based logic and memory applications.

| S-EPMC4756790 | biostudies-literature

Spin-dependent charge transport through 2D chiral hybrid lead-iodide perovskites.

Project description:Chiral-induced spin selectivity (CISS) occurs when the chirality of the transporting medium selects one of the two spin ½ states to transport through the media while blocking the other. Monolayers of chiral organic molecules demonstrate CISS but are limited in their efficiency and utility by the requirement of a monolayer to preserve the spin selectivity. We demonstrate CISS in a system that integrates an inorganic framework with a chiral organic sublattice inducing chirality to the hybrid system. Using magnetic conductive-probe atomic force microscopy, we find that oriented chiral 2D-layered Pb-iodide organic/inorganic hybrid perovskite systems exhibit CISS. Electron transport through the perovskite films depends on the magnetization of the probe tip and the handedness of the chiral molecule. The films achieve a highest spin-polarization transport of up to 86%. Magnetoresistance studies in modified spin-valve devices having only one ferromagnet electrode confirm the occurrence of spin-dependent charge transport through the organic/inorganic layers.

| S-EPMC6897542 | biostudies-literature

Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label c.

Project description:The influence of structural changes of an abasic site in duplex DNA on noncovalent and site-directed spin labeling (NC-SDSL) of the spin label ç were examined with electron paramagnetic resonance (EPR) spectroscopy. The binding affinities of ç to sixteen different DNA duplexes containing all possible sequences immediately flanking the abasic site were determined and the results showed that the binding of ç is highly flanking-sequence dependent. In general, a 5'-dG nucleotide favors the binding of the spin label. In particular, 5'-d(G__T) was the best binding sequence whereas 5'-d(C__T) showed the lowest affinity. Changing the structure of the abasic site linker from a tetrahydrofuran analog (F) to the anucleosidic C(3)-spacer (C(3)) does not appreciably affect the binding of ç to the abasic site. For efficient binding of ç, the abasic site needs to be located at least four base pairs away from the duplex end. Introducing a methyl substituent at N3 of ç did not change the binding affinity, but a decreased binding was observed for both N3-ethyl and -propyl groups. These results will guide the design of abasic site receptors and spin label ligands for NC-SDSL of nucleic acids.

| S-EPMC3333849 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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