Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biphasic DNA synthesis in spumaviruses.

ABSTRACT: Spumaviruses are complex retroviruses whose replication cycle resembles that of hepadnaviruses, especially by a late-occurring reverse transcription step. The possible existence of an early reverse transcription as observed in other retroviruses was not documented. Using real-time quantitative PCR, we addressed directly the kinetics of DNA synthesis during spumavirus infection. An early phase of viral DNA synthesis developed until 3 h postinfection, followed by a second phase, culminating 10 h postinfection. Both phases were abolished by the reverse transcriptase inhibitor 3'-azido-3'-deoxythymidine. Similar to other retroviruses, circular forms of viral DNA harboring two long terminal repeats were mainly found in the nucleus of infected cells. Interestingly, a fraction of these circular forms were detected in the cytoplasm and in extracellular virions, a feature shared with hepadnaviruses. Combined with packaging of both viral DNA and RNA genomes in virions, early and late reverse transcription might allow spumavirus to maximize its genome replication.

SUBMITTER: Delelis O

PROVIDER: S-EPMC161954 | biostudies-other | 2003 Jul

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Biphasic electrochemical peptide synthesis.

Project description:The large amount of waste derived from coupling reagents is a serious drawback of peptide synthesis from a green chemistry viewpoint. To overcome this issue, we report an electrochemical peptide synthesis in a biphasic system. Anodic oxidation of triphenylphosphine (Ph3P) generates a phosphine radical cation, which serves as the coupling reagent to activate carboxylic acids, and produces triphenylphosphine oxide (Ph3P[double bond, length as m-dash]O) as a stoichiometric byproduct. In combination with a soluble tag-assisted liquid-phase peptide synthesis, the selective recovery of desired peptides and Ph3P[double bond, length as m-dash]O was achieved. Given that methods to reduce Ph3P[double bond, length as m-dash]O to Ph3P have been reported, Ph3P[double bond, length as m-dash]O could be a recyclable byproduct unlike byproducts from typical coupling reagents. Moreover, a commercial peptide active pharmaceutical ingredient (API), leuprorelin, was successfully synthesized without the use of traditional coupling reagents.

| S-EPMC8513919 | biostudies-literature

First characterization of a biphasic, switch-like DNA amplification.

Project description:We report the first DNA amplification chemistry with switch-like characteristics: the chemistry is biphasic, with an expected initial phase followed by an unprecedented high gain burst of product oligonucleotide in a second phase. The first and second phases are separated by a temporary plateau, with the second phase producing 10 to 100 times more product than the first. The reaction is initiated when an oligonucleotide binds and opens a palindromic looped DNA template with two binding domains. Upon loop opening, the oligonucleotide trigger is rapidly amplified through cyclic extension and nicking of the bound trigger. Loop opening and DNA association drive the amplification reaction, such that reaction acceleration in the second phase is correlated with DNA association thermodynamics. Without a palindromic sequence, the chemistry resembles the exponential amplification reaction (EXPAR). EXPAR terminates at the initial plateau, revealing a previously unknown phenomenon that causes early reaction cessation in this popular oligonucleotide amplification reaction. Here we present two distinct types of this biphasic reaction chemistry and propose dominant reaction pathways for each type based on thermodynamic arguments. These reactions create an endogenous switch-like output that reacts to approximately 1 pM oligonucleotide trigger. The chemistry is isothermal and can be adapted to respond to a broad range of input target molecules such as proteins, genomic bacterial DNA, viral DNA, and microRNA. This rapid DNA amplification reaction could potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.

| S-EPMC5969907 | biostudies-literature

A mathematical model for a biphasic DNA amplification reaction.

Project description:Isothermal DNA amplification reactions are a prevalent tool with many applications, ranging from analyte detection to DNA circuits. Exponential amplification reaction (EXPAR) is a popular isothermal DNA amplification method that exponentially amplifies short DNA oligonucleotides. A recent modification of this technique using an energetically stable looped template with palindromic binding regions demonstrated unexpected biphasic amplification and much higher DNA yield than EXPAR. This ultrasensitive DNA amplification reaction (UDAR) shows high-gain, switch-like DNA output from low concentrations of DNA input. Here we present the first mathematical model of UDAR based on four reaction mechanisms and show the model can reproduce the experimentally observed biphasic behaviour. Furthermore, we show that three of these mechanisms are necessary to reproduce biphasic experimental results. The reaction mechanisms are (i) positively cooperative multistep binding spurred by two trigger binding sites on the template; (ii) gradual template deactivation; (iii) recycling of deactivated templates into active templates; and (iv) polymerase sequestration. These mechanisms can potentially illuminate the behaviour of EXPAR as well as other nucleic acid amplification reactions.

| S-EPMC6544893 | biostudies-literature

Strain-specific effect on biphasic DNA binding by HIV-1 integrase.

Project description:: The oligomerization of HIV-1 integrase onto DNA is not well understood. Here we show that HIV-1 integrase binds the DNA in biphasic (high-affinity and low-affinity) modes. For HIV-1 subtype B, the high-affinity mode is ∼100-fold greater than the low-affinity mode (Kd.DNA = 37 and 3400 nmol/l, respectively). The Kd.DNA values of patient-derived integrases containing subtype-specific polymorphisms were affected two- to four-fold, suggesting that polymorphisms may have an influence on effective-concentrations of inhibitors, as these inhibitors preferably bind to integrase-DNA complex.

| S-EPMC6472922 | biostudies-literature

Biphasic chromatin binding of histone chaperone FACT during eukaryotic chromatin DNA replication.

Project description:The facilitates chromatin transcription (FACT) complex affects nuclear DNA transactions in a chromatin context. Though the involvement of FACT in eukaryotic DNA replication has been revealed, a clear understanding of its biochemical behavior during DNA replication still remains elusive. Here, we analyzed the chromatin-binding dynamics of FACT using Xenopus egg extract cell-free system. We found that FACT has at least two distinct chromatin-binding phases: (1) a rapid chromatin-binding phase at the onset of DNA replication that did not involve origin licensing and (2) a second phase of chromatin binding that initiated after origin licensing. Intriguingly, early-binding FACT dissociated from chromatin when DNA replication was blocked by the addition of Cdc6 in the licensed state before origin firing. Cdc6-induced removal of FACT was blocked by the inhibition of origin licensing with geminin, but not by suppressing the activity of DNA polymerases, CDK, or Cdc7. Furthermore, chromatin transfer experiments revealed that impairing the later binding of FACT severely compromises DNA replication activity. Taken together, we propose that even though FACT has rapid chromatin-binding activity, the binding pattern of FACT on chromatin changes after origin licensing, which may contribute to the establishment of its functional link to the DNA replication machinery.

| S-EPMC3428913 | biostudies-literature

High-Yield 5-Hydroxymethylfurfural Synthesis from Crude Sugar Beet Juice in a Biphasic Microreactor.

Project description:5-Hydroxymethylfurfural (HMF) is an important biobased platform chemical obtainable in high selectivity by the hydrolysis of fructose (FRC). However, FRC is expensive, making the production of HMF at a competitive market price highly challenging. Here, it is shown that sugar beet thick juice, a crude, sucrose-rich intermediate in sugar refining, is an excellent feedstock for HMF synthesis. Unprecedented high selectivities and yields of >90 % for HMF were achieved in a biphasic reactor setup at 150 °C using salted diluted thick juice with H2 SO4 as catalyst and 2-methyltetrahydrofuran as a bioderived extraction solvent. The conversion of glucose, obtained by sucrose inversion, could be limited to <10 mol %, allowing its recovery for further use. Interestingly, purified sucrose led to significantly lower HMF selectivity and yields, showing advantages from both an economic and chemical selectivity perspective. This opens new avenues for more cost-effective HMF production.

| S-EPMC6790971 | biostudies-literature

Rhodium nanoparticles inside well-defined unimolecular amphiphilic polymeric nanoreactors: synthesis and biphasic hydrogenation catalysis.

Project description:Rhodium nanoparticles (Rh NPs) embedded in different amphiphilic core-crosslinked micelle (CCM) latexes (RhNP@CCM) have been synthesized by [RhCl(COD)(TPP@CCM)] reduction with H2 (TPP@CCM = core-anchored triphenylphosphine). The reduction rate depends on temperature, on the presence of base (NEt3) and on the P/Rh ratio. For CCMs with outer shells made of neutral P(MAA-co-PEOMA) copolymer chains (RhNP@CCM-N), the core-generated Rh NPs tend to migrate toward the hydrophilic shell and to agglomerate depending on the P/Rh ratio and core TPP density, whereas the MAA protonation state has a negligible effect. Conversely, CCMs with outer shells made of polycationic P(4VPMe+I-) chains (RhNP@CCM-C) maintain core-confined and well dispersed Rh NPs. All RhNP@CCMs were used as catalytic nanoreactors under aqueous biphasic conditions for acetophenone, styrene and 1-octene hydrogenation. Styrene was efficiently hydrogenated by all systems with high selectivity for vinyl reduction. For acetophenone, competition between benzene ring and carbonyl reduction was observed as well as a limited access to the catalytic sites when using CCM-C. Neat 1-octene was also converted, but the activity increased when the substrate was diluted in 1-nonanol, which is a better core-swelling solvent. Whereas the molecular RhI center was more active than the Rh0 NPs in 1-octene hydrogenation, the opposite trend was observed for styrene hydrogenation. Although Rh NP migration and agglomeration occurred for RhNP@CCM-N, even at high P/Rh, the NPs remained core-confined for RhNP@CCM-C, but only when toluene rather than diethyl ether was used for product extraction before recycling.

| S-EPMC9419193 | biostudies-literature

Biphasic Sol-Gel Synthesis of Microstructured/Nanostructured YVO4:Eu3+ Materials and Their H2O2 Sensing Ability.

Project description:Microstructured/nanostructured YVO4:Eu3+ powders and films were synthesized through a biphasic sol-gel method, aiming at their application as H2O2 sensing materials based on the turn-off luminescence of Eu3+ ions. The synthesis was typically carried out at temperatures of 80 °C or lower by using organic solutions to dissolve vanadium alkoxide and aqueous solutions to dissolve yttrium and europium salts together with sodium carboxylates. The resultant crystalline YVO4:Eu3+ powders and films were characterized as containing micrometer-sized particles comprising primary nanoparticles with high specific surface areas. A comparative study was performed on the H2O2-responsive turn-off luminescence properties for the above samples and those synthesized by a single-phase sol-gel or a conventional solid-state reaction method. The results indicated that the microstructural feature of the samples from the biphasic sol-gel method was effective for detecting H2O2 through its adsorption on the particle surface and quenching of the Eu3+ luminescence. The film samples showed repeatable and quantitative turn-off luminescence, thereby demonstrating their suitability as solid-state H2O2 sensors.

| S-EPMC6894179 | biostudies-literature

Positive feedback drives a secondary nonlinear product burst during a biphasic DNA amplification reaction.

Project description:Isothermal DNA amplification reactions are used in a broad variety of applications, from diagnostic assays to DNA circuits, with greater speed and less complexity than established PCR technologies. We recently reported a unique, high gain, biphasic isothermal DNA amplification reaction, called the Ultrasensitive DNA Amplification Reaction (UDAR). Here we present a detailed analysis of the UDAR reaction pathways that initiates with a first phase followed by a nonlinear product burst, which is caused by an autocatalytic secondary reaction. The experimental reaction output was reproduced using an ordinary differential equation model based on detailed reaction mechanisms. This model provides insight on the relative importance of each reaction mechanism during both phases, which could aid in the design of product output during DNA amplification reactions.

| S-EPMC10026376 | biostudies-literature

Biphasic unbinding of a metalloregulator from DNA for transcription (de)repression in Live Bacteria.

Project description:Microorganisms use zinc-sensing regulators to alter gene expression in response to changes in the availability of zinc, an essential micronutrient. Under zinc-replete conditions, the Fur-family metalloregulator Zur binds to DNA tightly in its metallated repressor form to Zur box operator sites, repressing the transcription of zinc uptake transporters. Derepression comes from unbinding of the regulator, which, under zinc-starvation conditions, exists in its metal-deficient non-repressor forms having no significant affinity with Zur box. While the mechanism of transcription repression by Zur is well-studied, little is known on how derepression by Zur could be facilitated. Using single-molecule/single-cell measurements, we find that in live Escherichia coli cells, Zur's unbinding rate from DNA is sensitive to Zur protein concentration in a first-of-its-kind biphasic manner, initially impeded and then facilitated with increasing Zur concentration. These results challenge conventional models of protein unbinding being unimolecular processes and independent of protein concentration. The facilitated unbinding component likely occurs via a ternary complex formation mechanism. The impeded unbinding component likely results from Zur oligomerization on chromosome involving inter-protein salt-bridges. Unexpectedly, a non-repressor form of Zur is found to bind chromosome tightly, likely at non-consensus sequence sites. These unusual behaviors could provide functional advantages in Zur's facile switching between repression and derepression.

| S-EPMC7049717 | 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