Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

"Click handle"-modified 2'-deoxy-2'-fluoroarabino nucleic acid as a synthetic genetic polymer capable of post-polymerization functionalization.

ABSTRACT: The functions of natural nucleic acids such as DNA and RNA have transcended genetic information carriers and now encompass affinity reagents, molecular catalysts, nanostructures, data storage, and many others. However, the vulnerability of natural nucleic acids to nuclease degradation and the lack of chemical functionality have imposed a significant constraint on their ever-expanding applications. Herein, we report the synthesis and polymerase recognition of a 5-(octa-1,7-diynyl)uracil 2'-deoxy-2'-fluoroarabinonucleic acid (FANA) triphosphate. The DNA-templated, polymerase-mediated primer extension using this "click handle"-modified FANA (cmFANA) triphosphate and other FANA nucleotide triphosphates consisting of canonical nucleobases efficiently generated full-length products. The resulting cmFANA polymers exhibited excellent nuclease resistance and the ability to undergo efficient click conjugation with azide-functionalized molecules, thereby becoming a promising platform for serving as a programmable and evolvable synthetic genetic polymer capable of post-polymerization functionalization.

SUBMITTER: Wu KB

PROVIDER: S-EPMC9200136 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Stepwise triple-click functionalization of synthetic peptides.

Project description:The increasing popularity of peptides as promising molecular scaffolds for biomedical applications and as valuable biochemical probes makes new methods allowing for their modification highly desirable. We describe herein an optimized protocol based on a sequence of CuAAC click reactions and selective deprotection steps, which leads to an efficient multi-functionalization of synthetic peptides. The methodology has been successfully applied to the construction of defined heteroglycopeptides and fluorophore-quencher-containing probes for proteases. The developed chemistry thus represents an important addition to the available toolbox of methods enabling efficient postsynthetic modification of peptides. The commercial availability of numerous azide probes further greatly extends the application potential of the described methodology.

| S-EPMC6113709 | biostudies-literature

Click with a boronic acid handle: a neighboring group-assisted click reaction that allows ready secondary functionalization.

Project description:The feasibility of a neighboring boronic acid-facilitated facile condensation of an aldehyde is described. This reaction is bio-orthogonal, complete at room temperature within minutes, and suitable for bioconjugation chemistry. The boronic acid group serves the dual purpose of catalyzing the condensation reaction and being a handle for secondary functionalization.

| S-EPMC4603419 | biostudies-literature

Pentafluorobenzene end-group as a versatile handle for <i>para</i> fluoro "click" functionalization of polythiophenes.

Project description:A convenient method of introducing pentafluorobenzene (PFB) as a single end-group in polythiophene derivatives is reported via in situ quenching of the polymerization. We demonstrate that the PFB-group is a particularly useful end-group due to its ability to undergo fast nucleophilic aromatic substitutions. Using this molecular handle, we are able to quantitatively tether a variety of common nucleophiles to the polythiophene backbone. The mild conditions required for the reaction allows sensitive functional moieties, such as biotin or a cross-linkable trimethoxysilane, to be introduced as end-groups. The high yield enabled the formation of a diblock rod-coil polymer from equimolar reactants under transition metal-free conditions at room temperature. We further demonstrate that water soluble polythiophenes end-capped with PFB can be prepared via the hydrolysis of an ester precursor, and that such polymers are amenable to functionalization under aqueous conditions.

| S-EPMC5408564 | biostudies-literature

Messenger RNA enrichment using synthetic oligo(T) click nucleic acids.

Project description:Enrichment of mRNA is a key step in a number of molecular biology techniques, particularly in the rapidly growing field of transcriptomics. Currently, mRNA is isolated using oligo(thymine) DNA (oligo(dT)) immobilized on solid supports, which binds to the poly(A) tail of mRNA to pull the mRNA out of solution through the use of magnets or centrifugal filters. Here, a simple method to isolate mRNA by complexing it with synthetic click nucleic acids (CNAs) is described. Oligo(T) CNA bound efficiently to mRNA, and because of the insolubility of CNA in water, >90% of mRNA was readily removed from solution using this method. Simple washing, buffer exchange, and heating steps enabled mRNA's enrichment from total RNA, with a yield of 3.1 ± 1.5% of the input total RNA by mass, comparable to the yield from commercially available mRNA enrichment beads. Further, the integrity and activity of mRNA after CNA-facilitated pulldown and release was evaluated through two assays. In vitro translation of EGFP mRNA confirmed the translatability of mRNA into functional protein and RT-qPCR was used to amplify enriched mRNA from total RNA extracts and compare gene expression to results obtained using commercially available products.

| S-EPMC7891491 | biostudies-literature

Synthesis and properties of 2'-deoxy-2',4'-difluoroarabinose-modified nucleic acids.

Project description:We report the synthesis, thermal stability, and RNase H substrate activity of 2'-deoxy-2',4'-difluoroarabino-modified nucleic acids. 2'-Deoxy-2',4'-difluoroarabinouridine (2,'4'-diF-araU) was prepared in a stereoselective way in six steps from 2'-deoxy-2'-fluoroarabinouridine (2'-F-araU). NMR analysis and quantum mechanical calculations at the nucleoside level reveal that introduction of 4'-fluorine introduces a strong bias toward the North conformation, despite the presence of the 2'-?F, which generally steers the sugar pucker toward the South/East conformation. Incorporation of the novel monomer into DNA results on a neutral to slightly stabilizing thermal effect on DNA-RNA hybrids. Insertion of 2',4'-diF-araU nucleotides in the DNA strand of a DNA-RNA hybrid decreases the rate of both human and HIV reverse transcriptase-associated RNase H-mediated cleavage of the complement RNA strand compared to that for an all-DNA strand or a DNA strand containing the corresponding 2'-F-araU nucleotide units, consistent with the notion that a 4'-fluorine in 2'-F-araU switches the preferred sugar conformation from DNA-like (South/East) to RNA-like (North).

| S-EPMC4484724 | biostudies-literature

Tailored Composite Polymer-Metal Nanoparticles by Miniemulsion Polymerization and Thiol-ene Functionalization.

Project description:A simple and modular synthetic approach, based on miniemulsion polymerization, has been developed for the fabrication of composite polymer-metal nanoparticle materials. The procedure produces well-defined composite structures consisting of gold, silver or MnFe(2)O(4) nanoparticles (∼10 nm in diameter) encapsulated within larger spherical nanoparticles of poly(divinylbenzene) (∼100 nm in diameter). This methodology readily permits the incorporation of multiple metal domains into a single polymeric particle, while still preserving the useful optical and magnetic properties of the metal nanoparticles. The morphology of the composite particles is retained upon increasing the inorganic content, and also upon redispersion in organic solvents. Finally, the ability to tailor the surface chemistry of the composite nanoparticles and incorporate steric stabilizing groups using simple thiol-ene chemistry is demonstrated.

| S-EPMC2908426 | biostudies-literature

Biofunctional Polymer Coated Au Nanoparticles Prepared via RAFT-Assisted Encapsulating Emulsion Polymerization and Click Chemistry.

Project description:The use of reversible addition-fragmentation chain transfer (RAFT)-assisted encapsulating emulsion polymerization (REEP) has been explored to prepare diverse types of colloidal stable core-shell nanostructures. A major field of application of such nanoparticles is in emergent nanomedicines, which require effective biofunctionalization strategies, in which their response to bioanalytes needs to be firstly assessed. Herein, functional core-shell nanostructures were prepared via REEP and click chemistry. Thus, following the REEP strategy, colloidal gold nanoparticles (Au NPs, d = 15 nm) were coated with a poly(ethylene glycol) methyl ether acrylate (PEGA) macroRAFT agent containing an azide (N3) group to afford N3-macroRAFT@Au NPs. Then, chain extension was carried out from the NPs surface via REEP, at 44 °C under monomer-starved conditions, to yield N3-copolymer@Au NPs-core-shell type structures. Biotin was anchored to N3-copolymer@Au NPs via click chemistry using an alkynated biotin to yield biofunctionalized Au nanostructures. The response of the ensuing biotin-copolymer@Au NPs to avidin was followed by visible spectroscopy, and the copolymer-biotin-avidin interaction was further studied using the Langmuir-Blodgett technique. This research demonstrates that REEP is a promising strategy to prepare robust functional core-shell plasmonic nanostructures for bioapplications. Although the presence of azide moieties requires the use of low polymerization temperature, the overall strategy allows the preparation of tailor-made plasmonic nanostructures for applications of biosensors based on responsive polymer shells, such as pH, temperature, and photoluminescence quenching. Moreover, the interaction of biotin with avidin proved to be time dependent.

| S-EPMC7408358 | biostudies-literature

Active Ester Containing Surfmer for One-Stage Polymer Nanoparticle Surface Functionalization in Mini-Emulsion Polymerization.

Project description:Functional surface active monomers (surfmers) are molecules that combine the functionalities of surface activity, polymerizability, and reactive groups. This study presents an improved pathway for the synthesis of the active ester containing surfmer p-(11-acrylamido)undecanoyloxyphenyl dimethylsulfonium methyl sulfate (AUPDS). Further, the preparation of poly(methyl methacrylate) and polystyrene nanoparticles (NPs) by mini-emulsion polymerization using AUPDS is investigated, leading to NPs with active ester groups on their surface. By systematically varying reaction parameters and reagent concentrations, it was found that AUPDS feed concentrations between 2⁻4 mol% yielded narrowly distributed and stable spherical particles with average sizes between 83 and 134 nm for non-cross-linked NPs, and up to 163 nm for cross-linked NPs. By basic hydrolysis of the active ester groups in aqueous dispersion, the positive ζ-potential (ZP) was converted into a negative ZP and charge quantities determined by polyelectrolyte titrations before and after hydrolysis were in the same range, indicating that the active ester groups were indeed accessible in aqueous suspension. Increasing cross-linker amounts over 10 mol% also led to a decrease of ZP of NPs, probably due to internalization of the AUPDS during polymerization. In conclusion, by using optimized reaction conditions, it is possible to prepare active ester functionalized NPs in one stage using AUPDS as a surfmer in mini-emulsion polymerization.

| S-EPMC6415249 | biostudies-literature

Post-synthesis DNA modifications using a trans-cyclooctene click handle.

Project description:Post-synthesis DNA modification is a very useful method for DNA functionalization. This is achieved by using a modified NTP, which has a handle for further modifications, replacing the corresponding natural NTP in polymerase-catalyzed DNA synthesis. Subsequently, the handle can be used for further functionalization after PCR, preferably through a very fast reaction. Herein we describe polymerase-mediated incorporation of trans-cyclooctene modified thymidine triphosphate (TCO-TTP). Subsequently, the trans-cyclooctene group was reacted with a tetrazine tethered to other functional groups through a very fast click reaction. The utility of this DNA functionalization method was demonstrated with the incorporation of a boronic acid group and a fluorophore. The same approach was also successfully used in modifying a known aptamer for fluorescent labelling applications.

| S-EPMC4377304 | biostudies-literature

Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies.

Project description:New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies.

| S-EPMC5075775 | 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