Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.

The RNA polymerase II (Pol II) elongation rate influences poly(A) site selection, with slow and fast Pol II derivatives causing upstream and downstream shifts, respectively, in poly(A) site utilization. In yeast, depletion of either of the histone chaperones FACT or Spt6 causes an upstream shift of poly(A) site use that strongly resembles the poly(A) profiles of slow Pol II mutant strains. Like slow Pol II mutant strains, FACT- and Spt6-depleted cells exhibit Pol II processivity defects, indicating that both Spt6 and FACT stimulate the Pol II elongation rate. Poly(A) profiles of some genes show atypical downstream shifts; this subset of genes overlaps well for FACT- or Spt6-depleted strains but is different from the atypical genes in Pol II speed mutant strains. In contrast, depletion of histone H3 or H4 causes a downstream shift of poly(A) sites for most genes, indicating that nucleosomes inhibit the Pol II elongation rate in vivo. Thus, chromatin-based control of the Pol II elongation rate is a potential mechanism, distinct from direct effects on the cleavage/polyadenylation machinery, to regulate alternative polyadenylation in response to genetic or environmental changes.

Divergent Polymer Superstructures from Protonated Poly(adenine) DNA and RNA.

Studies have shown that poly(adenine) DNA and RNA strands protonate at a low pH to form self-associating duplexes; however, the nanoscopic morphology of these structures is unclear. Here, we use Transition Electron Microscopy (TEM), Atomic Force Microscopy (AFM), dynamic light scattering (DLS), and fluorescence spectroscopy to show that both ribose identity (DNA or RNA) and assembly conditions (thermal or room-temperature annealing) dictate unique hierarchical structures for poly(adenine) sequences at a low pH. We show that while the thermodynamic product of protonating poly(adenine) DNA is a discrete dimer of two DNA strands, the kinetic product is a supramolecular polymer that branches and aggregates to form micron-diameter superstructures. In contrast, we find that protonated poly(A) RNA polymerizes into micrometer-length, twisted fibers under the same conditions. These divergent hierarchical morphologies highlight the amplification of subtle chemical differences between RNA and DNA into unique nanoscale behaviors. With the use of poly(adenine) strands spanning vaccine technologies, sensing, and dynamic biotechnology, understanding and controlling the underlying assembly pathways of these structures are critical to developing robust, programmable nanotechnologies.

Triblock PolyA-Mediated Protein Biosensor Based on a Size-Matching Proximity Hybridization Analysis.

The antibodies in the natural biological world utilize bivalency/multivalency to achieve a higher affinity for antigen capture. However, mimicking this mechanism on the electrochemical sensing interface and enhancing biological affinity through precise spatial arrangement of bivalent aptamer probes still pose a challenge. In this study, we have developed a novel self-assembly layer (SAM) incorporating triblock polyA DNA to enable accurate organization of the aptamer probes on the interface, constructing a "lock-and-key-like" proximity hybridization assay (PHA) biosensor. The polyA fragment acts as an anchoring block with a strong affinity for the gold surface. Importantly, it connects the two DNA probes, facilitating one-to-one spatial proximity and enabling a controllable surface arrangement. By precisely adjusting the length of the polyA fragment, we can tailor the distance between the probes to match the molecular dimensions of the target protein. This design effectively enhances the affinity of the aptamers. Notably, our biosensor demonstrates exceptional specificity and sensitivity in detecting PDGF-BB, as confirmed through successful validation using human serum samples. Overall, our biosensor presents a novel and versatile interface for proximity assays, offering a significantly improved surface arrangement and detection performance.

Efficient Poly-Adenine-Tailed DNA Functionalization of Gold Nanorods for Tailored Nanostructure Assembly.

Gold nanorods (AuNRs) with unique optical properties play a pivotal role in applications in plasmonic imaging, small molecule detection, and photothermal therapy. However, challenges in DNA functionalization of AuNRs hinder their full potential due to the presence of a dense cetyltrimethylammonium bromide (CTAB) bilayer, impeding close DNA contact. In this study, we introduced a convenient approach for the rapid assembly of polyadenine (polyA) tailed DNA on AuNRs with control of DNA density, rigidity, and valence. We explored the impact of DNA with designed properties on the construction of core-satellite structures by employing AuNRs as cores and spherical gold nanoparticles (AuNSs) as satellites. Density, rigidity, and valence are identified as crucial factors for efficient construction. Specifically, polyA-tailed DNA modulated DNA density and reduced spatial hindrance and electrostatic repulsion, thereby facilitating the construction. Enhancing the rigidity of DNA and incorporating multiple binding sites can further improve the efficiency.

Development of a label-free, sensitive gold nanoparticles-poly(adenine) aptasensing platform for colorimetric determination of aflatoxin B1 in corn.

In this work, a sensitive colorimetric bioassay method based on a poly(adenine) aptamer (polyA apt) and gold nanoparticles (AuNPs) was developed for the determination of aflatoxin B1 (AFB1). The polyA apt, adsorbed on the AuNPs, especially can bind to the analyte while deterring non-specific interactions. This nano aptasensor uses cationic polymer poly(diallyl dimethyl ammonium chloride) (PDDA), as an aggregating agent, to aggregate gold nanoparticles. PolyA apt-decorated gold nanoparticles (AuNPs/polyA apt) show resistance to PDDA-induced aggregation and maintains their dispersed state (red color) with the optical absorbance signal at λ = 520 nm. However, in the presence of AFB1 in the assay solution, the specific aptamer reacts with high affinity and folds into its three-dimensional form. Aggregation of AuNPs induced by PDDA caused their optical signal shift to λ = 620 nm (blue color). AFB1 concentration in the bioassay solution determines the amount of optical signal shift. Therefore, optical density ratio in two wavelengths (A620/520) can be used as a sturdy colorimetric signal to detect the concentration of aflatoxin B1. AFB1 was linearly detected between 0.5 and 20 ng mL-1, with a detection limit of 0.09 ng mL-1 (S/N = 3). The fabricated aptasensor was applied to the detection of AFB1 in real corn samples.

Renin imprinted Poly(methyldopa) for biomarker detection and disease therapy.

Conventional molecularly imprinted polymers (MIPs) perform their functions principally depended on their three dimensional (3D) imprinted cavities (recognition sites) of templates. Here, retaining the function of recognition sites resulted from the imprinting of template molecules, the role of functional monomers is explored and expanded. Briefly, a class of dual-functional renin imprinted poly(methyldopa) (RMIP) is prepared, consisting of a drug-type function monomer (methyldopa, clinical high blood pressure drug) and a corresponding disease biomarker (renin, biomarker for high blood pressure disease). To boost target-to-receptor binding ratio and sensitivity, the microstructure of recognition sites is beforehand calculated and designed by Density Functional Theory calculations, and the whole interfacial structure, property and thickness of RMIP film is regulated by adjusting the polymerization techniques. The dual-functional applications of RMIP for biomarker detection and disease therapy in vivo is explored. Such RMIP-based biosensors achieves highly sensitive biomarker detection, where the LODs reaches down to 1.31 × 10-6 and 1.26 × 10-6 ng mL-1 for electrochemical and chemical polymers, respectively, and the application for disease therapy in vivo has been verified where displays the obviously decreased blood pressure values of mice. No acute and long-term toxicity is found from the pathological slices, declaring the promising clinical application potential of such engineered RMIP nanostructure.

A strong and tough supramolecular assembled ß-cyclodextrin and chitin nanocrystals protein adhesive: Synthesis, characterization, bonding performance on three-layer plywood.

The development of a biomass adhesive as a substitute for petroleum-derived adhesives has been considered a viable option. However, achieving both superior bonding strength and toughness in biomass adhesives remains a significant challenge. Inspired by the human skeletal muscles structure, this study reveals a promising supramolecular structure using tannin acid (TA) functionalized poly-ß-cyclodextrin (PCD) (TA@PCD) as elastic tissues and chitin nanocrystals (ChNCs) as green reinforcements to strengthen the soybean meal (SM) adhesive crosslinking network. TA@PCD acts as a dynamic crosslinker that facilitates reversible host-guest interactions, hydrogen bonds, and electrostatic interactions between adjacent stiff ChNCs and SM matrix, resulting in satisfactory strength and toughness. The resulting SM/TA@PCD/ChNCs-2 adhesive has demonstrated satisfactory wet and dry shear strength (1.25 MPa and 2.57 MPa, respectively), toughness (0.69 J), and long-term solvents resistance (80 d). Furthermore, the adhesive can exhibit desirable antimildew characteristics owing to the phenol hydroxyl groups of TA and amino groups of ChNCs. This work showcases an effective supramolecular chemistry strategy for fabricating high-performance biomass adhesives with great potential for practical applications.

Fractionated lignin as a green compatibilizer to improve the compatibility of poly (butylene adipate-co-terephthalate) /polylactic acid composites.

Blending poly (butylene adipate-co-terephthalate) (PBAT) and polylactic acid (PLA) is a cost-effective strategy to obtain biodegradable plastic with complementary properties. However, the incompatibility between PBAT and PLA is a great challenge for fabricating high-performance composite films. Herein, the ethyl acetate fractionated lignin with the small glass transition temperature and low molecular weight was achieved and incorporated into the PBAT/PLA composite as a compatibilizer. The fractionated lignin can be uniformly dispersed within the PBAT/PLA matrix through a melt blending process and interact with the molecular chain of PBAT and PLA as a bonding bridge, which enhances the intermolecular interactions and reduces the interfacial tension of PBAT/PLA. By adding fractionated lignin, the tensile strength of the PBAT/PLA composite increased by 35.4 % and the yield strength increased by 37.7 %. Owing to lignin, the composite films possessed the ultraviolet shielding function and exhibited better water vapor barrier properties (1.73 ± 0.08 × 10-13 g·cm/cm2·s·Pa). This work conclusively demonstrated that fractionated lignin can be used as a green compatibilizer and a low-cost functional filler for PBAT/PLA materials, and provides guidance for the application of lignin in biodegradable plastics.

Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos.

During oocyte maturation and early embryogenesis, changes in mRNA poly(A)-tail lengths strongly influence translation, but how these tail-length changes are orchestrated has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with millions of 3' UTR sequence variants) in frog oocytes and embryos and in fish embryos. Contrasting to previously proposed cytoplasmic polyadenylation elements (CPEs), we found that a shorter element, UUUUA, together with the polyadenylation signal (PAS), specify cytoplasmic polyadenylation, and we identified contextual features that modulate the activity of both elements. In maturing oocytes, this tail lengthening occurs against a backdrop of global deadenylation and the action of C-rich elements that specify tail-length-independent translational repression. In embryos, cytoplasmic polyadenylation becomes more permissive, and additional elements specify waves of stage-specific deadenylation. Together, these findings largely explain the complex tapestry of tail-length changes observed in early frog and fish development, with strong evidence of conservation in both mice and humans.

Interaction of 3,9-disubstituted acridine with single stranded poly(rA), double stranded poly(rAU) and triple stranded poly(rUAU): molecular docking - A spectroscopic tandem study.

RNA plays an important role in many biological processes which are crucial for cell survival, and it has been suggested that it may be possible to inhibit individual processes involved in many diseases by targeting specific sequences of RNA. The aim of this work is to determine the affinity of novel 3,9-disubstited acridine derivative 1 with three different RNA molecules, namely single stranded poly(rA), double stranded homopolymer poly(rAU) and triple stranded poly(rUAU). The results of the absorption titration assays show that the binding constant of the novel derivative to the RNA molecules was in the range of 1.7-6.2 × 104 mol dm-3. The fluorescence and circular dichroism titration assays revealed considerable changes. The most significant results in terms of interpreting the nature of the interactions were the melting temperatures of the RNA samples in complexes with the 1. In the case of poly(rA), denaturation resulted in a self-structure formation; increased stabilization was observed for poly(rAU), while the melting points of the ligand-poly(rUAU) complex showed significant destabilization as a result of the interaction. The principles of molecular mechanics were applied to propose the non-bonded interactions within the binding complex, pentariboadenylic acid and acridine ligand as the study model. Initial molecular docking provided the input structure for advanced simulation techniques. Molecular dynamics simulation and cluster analysis reveal π - π stacking and the hydrogen bonds formation as the main forces that can stabilize the binding complex. Subsequent MM-GBSA calculations showed negative binding enthalpy accompanied the complex formation and proposed the most preferred conformation of the interaction complex.

Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes.

Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.

Rational design of an artificial tethered enzyme for non-templated post-transcriptional mRNA polyadenylation by the second generation of the C3P3 system.

We have previously introduced the first generation of C3P3, an artificial system that allows the autonomous in-vivo production of mRNA with m7GpppN-cap. While C3P3-G1 synthesized much larger amounts of capped mRNA in human cells than conventional nuclear expression systems, it produced a proportionately much smaller amount of the corresponding proteins, indicating a clear defect of mRNA translatability. A possible mechanism for this poor translatability could be the rudimentary polyadenylation of the mRNA produced by the C3P3-G1 system. We therefore sought to develop the C3P3-G2 system using an artificial enzyme to post-transcriptionally lengthen the poly(A) tail. This system is based on the mutant mouse poly(A) polymerase alpha fused at its N terminus with an N peptide from the λ virus, which binds to BoxBr sequences placed in the 3'UTR region of the mRNA of interest. The resulting system selectively brings mPAPαm7 to the target mRNA to elongate its poly(A)-tail to a length of few hundred adenosine. Such elongation of the poly(A) tail leads to an increase in protein expression levels of about 2.5-3 times in cultured human cells compared to the C3P3-G1 system. Finally, the coding sequence of the tethered mutant poly(A) polymerase can be efficiently fused to that of the C3P3-G1 enzyme via an F2A sequence, thus constituting the single-ORF C3P3-G2 enzyme. These technical developments constitute an important milestone in improving the performance of the C3P3 system, paving the way for its applications in bioproduction and non-viral human gene therapy.

Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution.

Shortening of messenger RNA poly(A) tails, or deadenylation, is a rate-limiting step in mRNA decay and is highly regulated during gene expression. The incorporation of non-adenosines in poly(A) tails, or 'mixed tailing', has been observed in vertebrates and viruses. Here, to quantitate the effect of mixed tails, we mathematically modeled deadenylation reactions at single-nucleotide resolution using an in vitro deadenylation system reconstituted with the complete human CCR4-NOT complex. Applying this model, we assessed the disrupting impact of single guanosine, uridine or cytosine to be equivalent to approximately 6, 8 or 11 adenosines, respectively. CCR4-NOT stalls at the 0, -1 and -2 positions relative to the non-adenosine residue. CAF1 and CCR4 enzyme subunits commonly prefer adenosine but exhibit distinct sequence selectivities and stalling positions. Our study provides an analytical framework to monitor deadenylation and reveals the molecular basis of tail sequence-dependent regulation of mRNA stability.

Strong and tough poly(vinyl alcohol)/xanthan gum-based ionic conducting hydrogel enabled through the synergistic effect of ion cross-linking and salting out.

The mechanical properties of ionic conductive hydrogels (ICHs) are generally inadequate, leading to their susceptibility to breakage under external forces and consequently resulting in the failure of flexible electronic devices. In this work, a simple and convenient strategy was proposed based on the synergistic effect of ion cross-linking and salting out, in which the hydrogels consisting of polyvinyl alcohol (PVA) and xanthan gum (XG) were immersed in zinc sulfate (ZnSO4) solution to obtain ICHs with exceptional mechanical properties. The salt-out effects between PVA chains and SO42- ions along with the cross-linked network of XG chains and Zn2+ ions contribute to the desirable mechanical properties of ICHs. Notably, the mechanical properties of ICHs can be adjusted by changing the concentration of ZnSO4 solution. Consequently, the optimum fracture stress and the fracture energy can reach 3.38 MPa and 12.13 KJ m-2, respectively. Moreover, the ICHs demonstrated a favorable sensitivity (up to 2.05) when utilized as a strain sensor, exhibiting an accurate detection of human body movements across various amplitudes.

Biodegradable reactive compatibilizers for efficient in-situ compatibilization of poly (lactic acid)/poly (butylene adipate-terephthalate) blends.

The wide application of fully biodegradable polylactic acid/polybutylene terephthalate (PLA/PBAT) blends in environmentally friendly packaging were limited because of poor compatibility. Normal compatibilizers suffer from poor thermal stability and non-biodegradability. In this work, epoxy copolymer (MDOG) with different molecular structures were made of 2-methylene-1, 3-dioxoheptane, and glycidyl methacrylate as raw materials by free radical copolymerization. MDOG copolymers have good biodegradability and a high thermal decomposition temperature of 361 °C. The chemical reaction of the epoxy groups in MDOG with PLA and PBAT during the melting reaction improved the interfacial bonding by decreasing the particle size of PBAT. Compared to the PLA/PBAT blends, the tensile strength and fracture toughness of PLA/PBAT/MDOG blends were enhanced to 34.6 MPa and 115.8 MJ/m3, which are 25 % and 81 % higher, respectively. As a result, this work offers new methods for developing thermally stable and biodegradable compatibilizers, which will hopefully promote the development of packaging industry.

Highly impact toughened and excellent flame-retardant polylactide/poly(butylene adipate-co-terephthalate) blend foams with phosphorus-containing and food waste-derived flame retardants.

Green polymeric foams are an important research topic for sustainable development. In this study, a natural multifunctional flame-retardant additive based on food waste was developed and evaluated for its ability to replace the commercial additives tricresyl phosphate (TCP) and trioctyl phosphate (TOP) in a polylactide/poly(butylene adipate-co-terephthalate) (PLA/PBAT) foam. A series of blend foams with additives were prepared by melt extrusion. According to the results, the blend foam with 20 phr of TCP showed the best combination of impact toughness and flame retardancy. TCP, however, poses health and environmental risks. Therefore, natural flame retardants (NFRs) were used to partially replace the commercial flame retardant (CFR). A combination of TCP and soybean residue (SB) produced an impact toughened and flame-retardant blend foam. When compared to the neat PLA/PBAT foam, the impact toughness of the best sample was increased by about 256 %. The optimal foam showed excellent flame resistance with a V-0 UL-94 rating and a high LOI value (31.8 %). SB has the potential to partially replace TCP as flame retardant and could be used in a broad range of PLA/PBAT foam applications.

Optimizing the Ion Conductivity and Mechanical Stability of Polymer Electrolyte Membranes Designed for Use in Lithium Ion Batteries: Combining Imidazolium-Containing Poly(ionic liquids) and Poly(propylene carbonate).

State-of-the-art Li batteries suffer from serious safety hazards caused by the reactivity of lithium and the flammable nature of liquid electrolytes. This work develops highly efficient solid-state electrolytes consisting of imidazolium-containing polyionic liquids (PILs) and lithium bis(trifluoromethane sulfonyl)imide (LiTFSI). By employing PIL/LiTFSI electrolyte membranes blended with poly(propylene carbonate) (PPC), we addressed the problem of combining ionic conductivity and mechanical properties in one material. It was found that PPC acts as a mechanically reinforcing component that does not reduce but even enhances the ionic conductivity. While pure PILs are liquids, the tricomponent PPC/PIL/LiTFSI blends are rubber-like materials with a Young's modulus in the range of 100 MPa. The high mechanical strength of the material enables fabrication of mechanically robust free-standing membranes. The tricomponent PPC/PIL/LiTFSI membranes have an ionic conductivity of 10-6 S·cm-1 at room temperature, exhibiting conductivity that is two orders of magnitude greater than bicomponent PPC/LiTFSI membranes. At 60 °C, the conductivity of PPC/PIL/LiTFSI membranes increases to 10-5 S·cm-1 and further increases to 10-3 S·cm-1 in the presence of plasticizers. Cyclic voltammetry measurements reveal good electrochemical stability of the tricomponent PIL/PPC/LiTFSI membrane that potentially ranges from 0 to 4.5 V vs. Li/Li+. The mechanically reinforced membranes developed in this work are promising electrolytes for potential applications in solid-state batteries.

Measurement of Poly A Tail Length from Drosophila Larva Brain and Cell Line.

Polyadenylation is a crucial posttranscriptional modification that adds poly(A) tails to the 3' end of mRNA molecules. The length of the poly(A) tail is tightly regulated by cellular processes. Dysregulation of mRNA polyadenylation has been associated with abnormal gene expression and various diseases, including cancer, neurological disorders, and developmental abnormalities. Therefore, comprehending the dynamics of polyadenylation is vital for unraveling the complexities of mRNA processing and posttranscriptional gene regulation. This paper presents a method for measuring poly(A) tail lengths in RNA samples isolated from Drosophila larval brains and Drosophila Schneider S2 cells. We employed the guanosine/inosine (G/I) tailing approach, which involves the enzymatic addition of G/I residues at the 3' end of mRNA using yeast poly(A) polymerase. This modification protects the RNA's 3' end from enzymatic degradation. The protected full-length poly(A) tails are then reverse-transcribed using a universal antisense primer. Subsequently, PCR amplification is performed using a gene-specific oligo that targets the gene of interest, along with a universal sequence oligo used for reverse transcription. This generates PCR products encompassing the poly(A) tails of the gene of interest. Since polyadenylation is not a uniform modification and results in tails of varying lengths, the PCR products display a range of sizes, leading to a smear pattern on agarose gel. Finally, the PCR products are subjected to high-resolution capillary gel electrophoresis, followed by quantification using the sizes of the poly(A) PCR products and the gene-specific PCR product. This technique offers a straightforward and reliable tool for analyzing poly(A) tail lengths, enabling us to gain deeper insights into the intricate mechanisms governing mRNA regulation.

A Novel Fabrication of Heterogeneous Saponified Poly(Vinyl Alcohol)/Pullulan Blend Film for Improved Wound Healing Application.

In this study, a novel film of poly(vinyl alcohol) (PVA)/pullulan (PULL) with improved surface characteristics was prepared from poly(vinyl acetate) (PVAc)/PULL blend films with various mass ratios after the saponification treatment in a heterogeneous medium. According to proton nuclear magnetic resonance (1H-NMR), Fourier transform infrared, and X-ray diffraction results, it was established that the successful fabrication of saponified PVA/PULL (100/0, 90/10, and 80/20) films could be obtained from PVAc/PULL (100/0, 90/10, and 80/20) films, respectively, after 72 h saponification at 50 °C. The degree of saponification calculated from 1H-NMR analysis results showed that fully saponified PVA was obtained from all studied films. Improved hydrophilic characteristics of the saponified films were revealed by a water contact angle test. Moreover, the saponified films showed improved mechanical behavior, and the micrographs of saponified films showed higher surface roughness than the unsaponified films. This kind of saponified film can be widely used for biomedical applications. Moreover, the reported saponified film dressing extended the lifespan of dressing as determined by its self-healing capacity and considerably advanced in vivo wound-healing development, which was attributed to its multifunctional characteristics, meaning that saponified film dressings are promising candidates for full-thickness skin wound healing.