Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Labeling of Polymer Nanostructures for Medical Imaging: Importance of crosslinking extent, spacer length, and charge density.

ABSTRACT: Radiolabeling studies were employed to investigate the influence of structure on the efficiency of surface functionalization for poly(acrylic acid)-coated shell crosslinked nanoparticles (SCKs) with two types of amine-terminated DOTA chelators. An intricate interplay between the chemical and physical properties of both the DOTA derivative and the SCK nanostructures was revealed, demonstrating the importance of structural control.

SUBMITTER: Xu J

PROVIDER: S-EPMC2531250 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Labeling of Polymer Nanostructures for Medical Imaging: Importance of crosslinking extent, spacer length, and charge density.

Xu Jinqi J Sun Guorong G Rossin Raffaella R Hagooly Aviv A Li Zicheng Z Fukukawa Ken-Ichi KI Messmore Benjamin W BW Moore Dennis A DA Welch Michael J MJ Hawker Craig J CJ Wooley Karen L KL

Macromolecules 20070101 9

Radiolabeling studies were employed to investigate the influence of structure on the efficiency of surface functionalization for poly(acrylic acid)-coated shell crosslinked nanoparticles (SCKs) with two types of amine-terminated DOTA chelators. An intricate interplay between the chemical and physical properties of both the DOTA derivative and the SCK nanostructures was revealed, demonstrating the importance of structural control. ...[more]

PMID: 18779874

Similar Datasets

Protein structure prediction guided by crosslinking restraints--A systematic evaluation of the impact of the crosslinking spacer length.

Project description:Recent development of high-resolution mass spectrometry (MS) instruments enables chemical crosslinking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments have been used successfully for structure refinement and protein-protein docking. However, one formidable question is under which circumstances XL-MS data might be sufficient to determine a protein's tertiary structure de novo? Answering this question will not only include understanding the impact of XL-MS data on sampling and scoring within a de novo protein structure prediction algorithm, it must also determine an optimal crosslinker type and length for protein structure determination. While a longer crosslinker will yield more restraints, the value of each restraint for protein structure prediction decreases as the restraint is consistent with a larger conformational space. In this study, the number of crosslinks and their discriminative power was systematically analyzed in silico on a set of 2055 non-redundant protein folds considering Lys-Lys, Lys-Asp, Lys-Glu, Cys-Cys, and Arg-Arg reactive crosslinkers between 1 and 60Å. Depending on the protein size a heuristic was developed that determines the optimal crosslinker length. Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm. The results demonstrate that a distinct crosslinker length exists for which information content for de novo protein structure prediction is maximized. The sampling accuracy improves on average by 1.0 Å and up to 2.2 Å in the most prominent example. XL-MS restraints enable consistently an improved selection of native-like models with an average enrichment of 2.1.

| S-EPMC4803439 | biostudies-literature

In situ Surface Charge Density Visualization of Self-assembled DNA Nanostructures after Ion Exchange.

Project description:The charge density of DNA is a key parameter in strand hybridization and for the interactions occurring between DNA and molecules in biological systems. Due to the intricate structure of DNA, visualization of the surface charge density of DNA nanostructures under physiological conditions was not previously possible. Here, we perform a simultaneous analysis of the topography and surface charge density of DNA nanostructures using atomic force microscopy and scanning ion conductance microscopy. The effect of in?situ ion exchange using various alkali metal ions is tested with respect to the adsorption of DNA origami onto mica, and a quantitative study of surface charge density reveals ion exchange phenomena in mica as a key parameter in DNA adsorption. This is important for structure-function studies of DNA nanostructures. The research provides an efficient approach to study surface charge density of DNA origami nanostructures and other biological molecules at a single molecule level.

| S-EPMC7891384 | biostudies-literature

Protein labeling and crosslinking by covalent aptamers.

Project description:In this chapter, a new approach to the selective modification of native proteins is discussed, using electrophilic covalent aptamers. These biochemical tools are generated through the site-specific incorporation of a label-transferring or crosslinking electrophile into a DNA aptamer. Covalent aptamers provide the ability to transfer a variety of functional handles to a protein of interest or to irreversibly crosslink to the target. Methods for the aptamer-mediated labeling and crosslinking of thrombin are described. Thrombin labeling is fast and selective, in both simple buffer and in human plasma and outcompetes nuclease-mediated degradation. This approach provides facile, sensitive detection of labeled protein by western blot, SDS-PAGE, and mass spectrometry.

| S-EPMC10725707 | biostudies-literature

Protein Labeling and Crosslinking by Covalent Aptamers.

Project description:We developed a new approach to selectively modify native proteins in their biological environment using electrophilic covalent aptamers. These aptamers are generated through introduction of a proximity-driven electrophile at specific nucleotide sites. Using thrombin as a proof-of-concept, we demonstrate that covalent aptamers can selectively transfer a variety of functional handles and/or irreversibly crosslink to the target protein. This approach offers broad programmability and high target specificity. Furthermore, it addresses issues common to aptamers such as instability towards endogenous nucleases and residence times during target engagement. Covalent aptamers are new tools that enable specific protein modification and sensitive protein detection. Moreover, they provide prolonged, nuclease-resistant enzyme inhibition.

| S-EPMC8260448 | biostudies-literature

Mapping Optimal Charge Density and Length of ROMP-Based PTDMs for siRNA Internalization.

Project description:A fundamental understanding of how polymer structure impacts internalization and delivery of biologically relevant cargoes, particularly small interfering ribonucleic acid (siRNA), is of critical importance to the successful design of improved delivery reagents. Herein we report the use of ring-opening metathesis polymerization (ROMP) methods to synthesize two series of guanidinium-rich protein transduction domain mimics (PTDMs): one based on an imide scaffold that contains one guanidinium moiety per repeat unit, and another based on a diester scaffold that contains two guanidinium moieties per repeat unit. By varying both the degree of polymerization and, in effect, the relative number of cationic charges in each PTDM, the performances of the two ROMP backbones for siRNA internalization were evaluated and compared. Internalization of fluorescently labeled siRNA into Jurkat T cells demonstrated that fluorescein isothiocyanate (FITC)-siRNA internalization had a charge content dependence, with PTDMs containing approximately 40 to 60 cationic charges facilitating the most internalization. Despite this charge content dependence, the imide scaffold yielded much lower viabilities in Jurkat T cells than the corresponding diester PTDMs with similar numbers of cationic charges, suggesting that the diester scaffold is preferred for siRNA internalization and delivery applications. These developments will not only improve our understanding of the structural factors necessary for optimal siRNA internalization, but will also guide the future development of optimized PTDMs for siRNA internalization and delivery.

| S-EPMC5094354 | biostudies-literature

Superior Charge Storage and Power Density of a Conducting Polymer-Modified Covalent Organic Framework.

Project description:The low conductivity of two-dimensional covalent organic frameworks (2D COFs), and most related coordination polymers, limits their applicability in optoelectronic and electrical energy storage (EES) devices. Although some networks exhibit promising conductivity, these examples generally lack structural versatility, one of the most attractive features of framework materials design. Here we enhance the electrical conductivity of a redox-active 2D COF film by electropolymerizing 3,4-ethylenedioxythiophene (EDOT) within its pores. The resulting poly(3,4-ethylenedioxythiophene) (PEDOT)-infiltrated COF films exhibit dramatically improved electrochemical responses, including quantitative access to their redox-active groups, even for 1 ?m-thick COF films that otherwise provide poor electrochemical performance. PEDOT-modified COF films can accommodate high charging rates (10-1600 C) without compromising performance and exhibit both a 10-fold higher current response relative to unmodified films and stable capacitances for at least 10?000 cycles. This work represents the first time that electroactive COFs or crystalline framework materials have shown volumetric energy and power densities comparable with other porous carbon-based electrodes, thereby demonstrating the promise of redox-active COFs for EES devices.

| S-EPMC5043428 | biostudies-literature

Fabrication of triboelectric polymer films via repeated rheological forging for ultrahigh surface charge density.

Project description:Triboelectric polymer with high charge density is the foundation to promote the wide range of applications of triboelectric nanogenerators. This work develops a method to produce triboelectric polymer based on repeated rheological forging. The fluorinated ethylene propylene film fabricated by repeated forging method not only has excellent mechanical properties and good transmittance, but also can maintain an ultrahigh tribo-charge density. Based on the film with a thickness of 30 μm, the output charge density from contact-separation nanogenerator reaches 352 μC·m-2. Then, the same film is applied for the nanogenerator with air-breakdown mode and a charge density of 510 μC·m-2 is further achieved. The repeated forging method can effectively regulate the composition of surface functional groups, the crystallinity, and the dielectric constants of the fluorinated ethylene propylene, leading to the superior capability of triboelectrification. Finally, we summarize the key parameters for elevating the electrification performance on the basis of molecular structure and related fabrication crafts, which can guide the further development of triboelectric polymers.

| S-EPMC9283396 | biostudies-literature

Importance of having low-density functional groups for generating high-performance semiconducting polymer dots.

Project description:Semiconducting polymers with low-density side-chain carboxylic acid groups were synthesized to form stable, functionalized, and highly fluorescent polymer dots (Pdots). The influence of the molar fraction of hydrophilic side-chains on Pdot properties and performance was systematically investigated. Our results show that the density of side-chain carboxylic acid groups significantly affects Pdot stability, internal structure, fluorescence brightness, and nonspecific binding in cellular labeling. Fluorescence spectroscopy, single-particle imaging, and a dye-doping method were employed to investigate the fluorescence brightness and the internal structure of the Pdots. The results of these experiments indicate that semiconducting polymers with low density of side-chain functional groups can form stable, compact, and highly bright Pdots as compared to those with high density of hydrophilic side-chains. The functionalized polymer dots were conjugated to streptavidin (SA) by carbodiimide-catalyzed coupling and the Pdot-SA probes effectively and specifically labeled the cancer cell-surface marker Her2 in human breast cancer cells. The carboxylate-functionalized polymer could also be covalently modified with small functional molecules to generate Pdot probes for click chemistry-based bio-orthogonal labeling. This study presents a promising approach for further developing functional Pdot probes for biological applications.

| S-EPMC3383935 | biostudies-literature

Photoaffinity labeling of transcription factors by DNA-templated crosslinking.

Project description:Characterization of transcription factor-DNA interaction is of high importance in elucidating the molecular mechanisms of gene transcriptions. DNA-based affinity probes were developed to capture and identify transcription factors by covalent crosslinking; however, the requirement of a crosslinker on the affinity probe remains a disadvantage, as the crosslinker itself often interferes with the protein-DNA interactions. We report a dual-probe method able to capture DNA-binding transcription factors with unmodified protein-binding sites in scenarios where conventional probes have failed. We have also shown the method's converse application in selecting specific transcription factor-binding DNA sequences from a probe library and its extension to studying proteins recognizing epigenetic marks. This study may provide a new tool for exploring DNA-binding proteins in biology.

| S-EPMC5494549 | biostudies-literature

Para-aminobenzamidine linked regenerated cellulose membranes for plasminogen activator purification: effect of spacer arm length and ligand density.

Project description:Despite membrane-based separations offering superior alternative to packed bed chromatographic processes, there has been a substantial lacuna in their actual application to separation processes. One of the major reasons behind this is the lack of availability of appropriately modified or end-group modifiable membranes. In this paper, an affinity membrane was developed using a commercially available serine protease inhibitor, para-aminobenzamidine (pABA). The membrane modification was optimized for protein binding capacity by varying: (i) the length of the spacer arm (SA; 5-atoms, 7-atoms, and 14-atoms) linking the ligand to membrane surface; (ii) the affinity ligand (pABA) density on membrane surface (5-25nmol/cm(2)). Resulting membranes were tested for their ability to bind plasminogen activators (PAs) from mono- and multi-component systems in batch mode. The membrane containing pABA linked through 7-atoms SA but similar ligand density as in the case of 5- or 14-atoms long SA was found to bind up to 1.6-times higher amounts of PA per nmoles of immobilized ligand from conditioned HeLa cell culture media. However, membranes with similar ligand densities but different lengths of SA, showed comparable binding capacities in mono-component system. In addition, the length of SA did not affect the selectivity of the ligand for PA. A clear inverse linear correlation was observed between ligand density and binding capacity until the point of PA binding optima was reached (11±1.0nmol/cm(2)) in mono- and multi-component systems for 7- as well as 14-atoms SA. Up to 200-fold purification was achieved in a single step separation of PA from HeLa conditioned media using these affinity membranes. The issues of ligand leaching and reuse of the membranes were also investigated. An extensive regeneration procedure allowed the preservation of approximately 95% of the PA binding capacity of the membranes even after five cycles of use.

| S-EPMC3687526 | 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