Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reductive Charge Transfer through an RNA Aptamer.

ABSTRACT: The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non-Watson-Crick base-paired regions might be required. We here demonstrate distance-dependent reductive charge transfer through RNA duplexes and through the non-Watson-Crick base-paired region of an RNA aptamer.

SUBMITTER: Frommer J

PROVIDER: S-EPMC7756803 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Reductive Charge Transfer through an RNA Aptamer.

Frommer Jennifer J Müller Sabine S

Angewandte Chemie (International ed. in English) 20201013 51

The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transp ...[more]

PMID: 32852119

Similar Datasets

Investigation of Intramolecular Through-Space Charge-Transfer States in Donor-Acceptor Charge-Transfer Systems.

Project description:Commonly, thermally activated delayed fluorescence (TADF) emitters present a twisted donor-acceptor structure. Here, electronic communication is mediated through-bond via π-conjugation between donor and acceptor groups. A second class of TADF emitters are those where electronic communication between donor and acceptor moieties is mediated through-space. In these through-space charge-transfer (TSCT) architectures, the donor and acceptor groups are disposed in a pseudocofacial orientation and linked via a bridging group that is typically an arene (or heteroarene). In most of these systems, there is no direct evidence that the TSCT is the dominant contributor to the communication between the donor and acceptor. Herein we investigate the interplay between through-bond localized excited (LE) and charge-transfer (CT) states and the TSCT in a rationally designed emitter, TPA-ace-TRZ, and a family of model compounds. From our photophysical studies, TSCT TADF in TPA-ace-TRZ is unambiguously confirmed and supported by theoretical modeling.

| S-EPMC8041366 | biostudies-literature

Multifunctional Charge-Transfer Single Crystals through Supramolecular Assembly.

Project description:Centimeter-sized segregated stacking TTF-C60 single crystals are crystallized by a mass-transport approach combined with solvent-vapor evaporation for the first time. The intermolecular charge-transfer interaction in the long-range ordered superstructure enables the crystals to demonstrate external stimuli-controlled multifunctionalities and angle/electrical-potential-dependent luminescence.

| S-EPMC7798091 | biostudies-literature

Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer.

Project description:In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern with respect to conformational inhomogeneity. In this letter, we report studies on a different set of ethidium DNA conjugates. In contrast to the "Caltech systems," these conjugates contain ethidium tightly incorporated (as a base pair surrogate) into the DNA base stack, opposite to an abasic site analog. Despite the tight binding, we found that charge transfer from the photoexcited ethidium base pair surrogate across two or more base pairs is several orders of magnitude slower than in case of the DNA systems bearing the tethered ethidium. To further broaden the scope of this account, we compared (oxidative) electron hole transfer and (reductive) electron transfer using the same ethidium chromophore as a charge donor in combination with two different charge acceptors. We found that both electron and hole transfer are characterized by similar rates and distance dependencies. The results demonstrate the importance of nuclear motions and conformational flexibility and underline the presence of a base gating mechanism, which appears to be generic to electronic transfer processes through pi-stacked nucleic acids.

| S-EPMC1502433 | biostudies-literature

Charge transfer complexation boosts molecular conductance through Fermi level pinning.

Project description:Interference features in the transmission spectra can dominate charge transport in metal-molecule-metal junctions when they occur close to the contact Fermi energy (E F). Here, we show that by forming a charge-transfer complex with tetracyanoethylene (TCNE) we can introduce new constructive interference features in the transmission profile of electron-rich, thiophene-based molecular wires that almost coincide with E F. Complexation can result in a large enhancement of junction conductance, with very efficient charge transport even at relatively large molecular lengths. For instance, we report a conductance of 10-3 G 0 (∼78 nS) for the ∼2 nm long α-quaterthiophene:TCNE complex, almost two orders of magnitude higher than the conductance of the bare molecular wire. As the conductance of the complexes is remarkably independent of features such as the molecular backbone and the nature of the contacts to the electrodes, our results strongly suggest that the interference features are consistently pinned near to the Fermi energy of the metallic leads. Theoretical studies indicate that the semi-occupied nature of the charge-transfer orbital is not only important in giving rise to the latter effect, but also could result in spin-dependent transport for the charge-transfer complexes. These results therefore present a simple yet effective way to increase charge transport efficiency in long and poorly conductive molecular wires, with important repercussions in single-entity thermoelectronics and spintronics.

| S-EPMC6385675 | biostudies-literature

Dynamical treatment of charge transfer through duplex nucleic acids containing modified adenines.

Project description:We address the issue of whether chemical alterations of nucleobases are an effective tool to modulate charge transfer through DNA molecules. Our investigation uses a multilevel computational approach based on classical molecular dynamics and quantum chemistry. We find yet another piece of evidence that structural fluctuations are a key factor to determine the electronic structure of double-stranded DNA. We argue that the electronic structure and charge transfer ability of flexible polymers is the result of a complex intertwining of various structural, dynamical and chemical factors. Chemical intuition may be used to design molecular wires, but this is not the sole component in the complex charge transfer mechanism through DNA.

| S-EPMC3903158 | biostudies-literature

Inducing Charge Separation in Solid-State Two-Dimensional Hybrid Perovskites through the Incorporation of Organic Charge-Transfer Complexes.

Project description:Two-dimensional (2D) hybrid perovskites make up an emerging class of materials for optoelectronic applications in which inorganic octahedral layers are separated by nonconductive large organic cations. This leads to a high-dimensional and dielectric confinement and hence a high exciton binding energy, which severely limits their application in devices in which charge carrier separation is required. In this work, we achieve improved charge separation by replacing nonconductive organic cations with organic charge-transfer complexes consisting of a pyrene donor and a tetracyanoquinodimethane acceptor. Steady-state absorption measurements show that these materials exhibit optical features that match with the absorption of the organic charge-transfer complexes. Using microwave conductivity and femtosecond transient absorption, we show that photoexcitation of these charge-transfer states leads to long-lived mobile charges in the inorganic layers. While the efficiency of charge separation is relatively low, these experiments demonstrate that it is possible to induce charge separation in solid-state 2D perovskites by engineering the organic layer.

| S-EPMC7008460 | biostudies-literature

Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.

Project description:Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.

| S-EPMC8192780 | biostudies-literature

Charge Transfer Reductive <i>in situ</i> Doping of Mesoporous TiO<sub>2</sub> Photoelectrodes - Impact of Electrolyte Composition and Film Morphology.

Project description:Some material properties depend not only on synthesis and processing parameters, but may furthermore significantly change during operation. This is particularly true for high surface area materials. We used a combined electrochemical and spectroscopic approach to follow the changes of the photoelectrocatalytic activity and of the electronic semiconductor properties of mesoporous TiO2 films upon charge transfer reductive doping. Shallow donors (i.e. electron/proton pairs) were introduced into the semiconductor by the application of an external potential or, alternatively, by band gap excitation at open circuit conditions. In the latter case the effective open circuit doping potential depends critically on electrolyte composition (e.g. the presence of electron or hole acceptors). Transient charge accumulation (electrons and protons) in nanoparticle electrodes results in a photocurrent enhancement which is attributed to the deactivation of recombination centers. In nanotube electrodes the formation of a space charge layer results in an additional decrease of charge recombination at positive potentials. Doping is transient in nanoparticle films, but turns out to be stable for nanotube arrays.

| S-EPMC7116043 | biostudies-literature

Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195.

Project description:The genome of Dehalococcoides ethenogenes strain 195, an anaerobic dehalorespiring bacterium, contains 18 copies of putative reductive dehalogenase genes, including the well-characterized tceA gene, whose gene product functions as the key enzyme in the environmentally important dehalorespiration process. The genome of D. ethenogenes was analyzed using a bioinformatic tool based on the frequency of oligonucleotides. The results in the form of a genomic signature revealed several local disruptions of the host signature along the genome sequence. These fractures represent DNA segments of potentially foreign origin, so-called atypical regions, which may have been acquired by an ancestor through horizontal gene transfer. Most interestingly, 15 of the 18 reductive dehalogenase genes, including the tceA gene, were found to be located in these regions, strongly indicating the foreign nature of the dehalorespiration activity. The GC content and the presence of recombinase genes within some of these regions corroborate this hypothesis. A hierarchical classification of the atypical regions containing the reductive dehalogenase genes indicated that these regions were probably acquired by several gene transfer events.

| S-EPMC1151795 | biostudies-literature

Functional Charge Transfer Plasmon Metadevices.

Project description:Reducing the capacitive opening between subwavelength metallic objects down to atomic scales or bridging the gap by a conductive path reveals new plasmonic spectral features, known as charge transfer plasmon (CTP). We review the origin, properties, and trending applications of this modes and show how they can be well-understood by classical electrodynamics and quantum mechanics principles. Particularly important is the excitation mechanisms and practical approaches of such a unique resonance in tailoring high-response and efficient extreme-subwavelength hybrid nanophotonic devices. While the quantum tunneling-induced CTP mode possesses the ability to turn on and off the charge transition by varying the intensity of an external light source, the excited CTP in conductively bridged plasmonic systems suffers from the lack of tunability. To address this, the integration of bulk plasmonic nanostructures with optothermally and optoelectronically controllable components has been introduced as promising techniques for developing multifunctional and high-performance CTP-resonant tools. Ultimate tunable plasmonic devices such as metamodulators and metafilters are thus in prospect.

| S-EPMC7013279 | 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