Generation of ribosome imprinted polymers for sensitive detection of translational responses

Whilst the profiling of the transcriptome and proteome even of single-cells becomes feasible, the analysis of the translatome, which refers to all messenger RNAs (mRNAs) engaged with ribosomes for protein synthesis, is still an elaborate procedure requiring millions of cells. Herein, we report the generation and use of “smart materials”, namely molecularly imprinted polymers (MIPs) to facilitate the isolation of ribosomes and translated mRNAs from merely 1,000 cells. In particular, we show that a hydrogel-based ribosome imprinted polymer could recover ribosomes and associated mRNAs from human, simian and mice cellular extracts, but did not selectively enrich yeast ribosomes, thereby demonstrating selectivity. Furthermore, ribosome imprinted polymers enabled the sensitive measurement of an mRNA translational regulatory event, requiring 1,000-fold less cells than current methodologies. These results provide first evidence for the suitability of MIPs to selectively recover ribonucleoprotein complexes such as ribosomes, founding a novel means for sensitive detection of gene regulation

Nucleic acid-based fluorescent probes and their analytical potential

It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays

Voltammetric sensor for theophylline using sol-gel immobilized molecularly imprinted polymer particles

El títol del pre-print va ser: Development of a voltammetric sensor for theophylline with sol-gel immobilised molecularly imprinted polymer particlesApplication of Molecularly Imprinted Polymers (MIPs) to sensor substrates holds great promise within the field of electrochemical sensing due to their low price, tailored selectivity and facile synthesis protocols. Though MIPs can be synthesised directly onto the surface of sensors via layer or film deposition, this can be difficult due to the high number of interdependent steps involved in their synthesis. For this reason, synthesis of MIP particles is more frequently employed by synthetic and non-specialist laboratories alike. There is, however a lack of immobilisation protocols for these particles. Herein, there is presented a sol-gel based immobilisation method for MIP particles for the development of an electrochemical sensor. The macroporous precipitation-polymerised particles were imprinted with Theophylline, combined with graphite in the sol-gel and deposited on an electrode surface. The sensor was tested using differential pulse voltammetry. A limit of detection of 1µM and a relative standard deviation of 6.85% was observed for the primary analyte. The electrode was regenerated via a thermal washing process with a signal loss of 29.3% following the initial regeneration and 2.35% per subsequent regeneration

Application of molecularly imprinted polymer nanoparticles for degradation of the bacterial autoinducer N-hexanoyl homoserine lactone.

A novel bacterial quorum quenching system is presented. For the first time the degradation of N-l-hexanoyl homoserine lactone (C6-AHL), a Gram-negative quorum sensing autoinducer, has been enhanced using molecularly imprinted nanoparticles (MIP NPs) which were prepared using transition state analogue of the γ-lactone ring hydrolysis as template

Development of a homogenous assay based on fluorescent imprinted nanoparticles for analysis of nitroaromatic compounds

Herein we describe the development of a homogeneous assay for the detection of 4-nitroaniline (4-NA) and 2,4-dinitroaniline (2,4-diNA). This assay relies on fluorescent molecularly imprinted nanoparticles (nanoMIPs) which, upon interaction with the target analytes, generate a reduction in fluorescence emission intensity (quenching). This is due to a responsive fluorescent monomer (N-2-propenyl-(5-dimethylamino)-1-naphthalene sulphonamide) employed in the manufacture of the nanoMIPs which, by virtue of the imprinting process, is capable of selective interaction with the target analyte, thus giving rise to a quenching effect. Selectivity experiments showed excellent recognition properties toward the target molecule. Under optimal conditions, the fluorescence intensity of these nanoMIPs decreased as the concentration of the imprinted analyte increased from 10 nM to 2.71 μM. A linear relation between the negative logarithm of 4-NA or 2,4-diNA concentrations and the fluorescence intensity for both nanosystems was found (R2 = 0.991 and R2 = 0.9895), with excellent sensitivity (limit of detection (LOD) = 7 and 6 nM, respectively). Furthermore, both nanosystems have been successfully applied for detection of 4-NA or 2,4-diNA in tap water, with recoveries between 90% to 100.6% and 92% to 100.3%, respectively. Thanks to the versatility of the imprinting process, this nanosystem holds the potential for further development of several optical sensors for many other compounds. [Figure not available: see fulltext.].</p

New protocol for optimisation of polymer composition for imprinting of peptides and proteins

We present here a novel screening tool for optimisation of polymerisation mixtures used in imprinting of peptides and proteins. To facilitate rapid synthesis and screening of a combinatorial library of polymers the solid-phase synthesis method developed by Piletsky and co-workers was scaled down to 50 mg of template-immobilised solid phase, allowing a single well of a 96-well microplate to function as an individual reaction vessel. In this way, 32 different polymer compositions containing N-isopropylacrylamide, acrylic acid, N-(3-aminopropyl)methacrylamide hydrochloride, and N-tert-butylacrylamide, were tested in imprinting of three peptides and three proteins. Utilising filtration microplates has allowed the elution and washing steps to be performed in a similar manner to the large-scale synthesis, whilst incorporation of a fluorescent monomer (N-fluoresceinylacrylamide) made it possible to analyse the binding of synthesised polymer nanoparticles to the solid phase with immobilised templates under different washing conditions. The experiment has proven that the variations in monomer compositions had an effect on the yield and affinity of synthesised molecularly imprinted polymers for the peptides, but not for the proteins. Imprinting in this way presents an ideal method for performing small-scale syntheses for testing polymerisation mixtures, as information regarding the molecularly imprinted polymers affinity can be assessed as part of the elution process, without a need for time-consuming analysis such as quartz crystal microbalance or surface plasmon resonance