Effects of heterogeneous surface characteristics on hemocompatibility and cytocompatibility of bacterial nanocellulose.

The surface properties of cardiovascular biomaterials play a critical role in their biological responses. Although bacterial nanocellulose (BNC) materials have exhibited potential applications in cardiovascular implants, the impact of their surface characteristics on biocompatibility has rarely been studied. This study investigated the mechanism for the biocompatibility induced by the physicochemical properties of both sides of BNC. With greater wettability and smoothness, the upper BNC surface reduced protein adsorption by 25 % compared with the lower surface. This prolonged the plasma re-calcification time by 14 % in venous blood. Further, compared with the lower BNC surface, the upper BNC surface prolonged the activated partial thromboplastin time by 5 % and 4 % in arterial and venous blood, respectively. Moreover, the lower BNC surface with lesser rigidity, higher roughness, and sparser fiber structure promoted cell adhesion. The lower BNC surface enhanced the proliferation rate of L929 and HUVECs cells by 15 % and 13 %, respectively, compared with the upper BNC surface. With lesser stiffness, the lower BNC surface upregulated the expressions of CD31 and eNOS while down-regulating the ICAM-1 expression - This promoted the proliferation of HUVECs. The findings of this study will provide valuable insights into the design of blood contact materials and cardiovascular implants.

Chitosan particles embedded bacterial nanocellulose flat membrane for hemodialysis.

The development of bio-based hemodialysis membranes continues to be a challenge. Bacterial nanocellulose (BNC) membranes show potential in hemodialysis but can hardly retain beneficial proteins. Here, chitosan particles/bacterial nanocellulose (CSP/BNC) membranes were designed to efficiently remove uremic toxins and retain beneficial proteins. First, CSPs were synthesized in situ within a BNC membrane by ionic gelation following negative pressure impregnation. Subsequently, these membranes were thoroughly characterized. Compared with the BNC membrane, the pore volume and pore size of the 3 % CSP/BNC membrane decreased by 42.2 % and 32.1 %, respectively. The increased 22.2 times of Young's modulus and 88.9 % of tensile strength in the 3 % CSP/BNC membrane confirmed enhanced mechanical property. The sieving coefficient of bovine serum albumin decreased to 0.05 ± 0.03 in the 3 % CSP/BNC membrane. Moreover, the CSP/BNC membrane exhibited good hemocompatibility and cytocompatibility. The simulated dialysis results showed that the 3 % CSP/BNC membrane exhibited high clearance of urea (16.37 %/cm2) and lysozyme (3.54 %/cm2), while efficiently retaining bovine serum albumin (98.04 %/cm2). This is the first demonstration of the construction of a BNC-based hemodialysis membrane with in situ CSP formation to effectively regulate the pore properties of the membrane, making the CSP/BNC membrane a promising candidate for hemodialysis applications.

In Silico and In Vitro Studies of 4-Hydroxycoumarin-Based Heterocyclic Enamines as Potential Anti-Tumor Agents.

The present study reports the one-step synthesis of several 3-formyl-4-hydroxycouramin-derived enamines (4a-4i) in good yields (65-94%). The characterization of the synthesized compounds was carried out via advanced analytical and spectroscopic techniques, such as melting point, electron impact mass spectrometry (EI-MS), 1H-NMR, 13C-NMR, elemental analysis, FTIR, and UV-Visible spectroscopy. The reaction conditions were optimized, and the maximum yield was obtained at 3-4 h of reflux of the reactants, using 2-butanol as a solvent. The potato disc tumor assay was used to assess Agrobacterium tumefaciens-induced tumors to evaluate the anti-tumor activities of compounds (4a-4i), using Vinblastine as a standard drug. The compound 4g showed the lowest IC50 value (1.12 ± 0.2), which is even better than standard Vinblastine (IC50 7.5 ± 0.6). For further insight into their drug actions, an in silico docking of the compounds was also carried out against the CDK-8 protein. The binding energy values of compounds were found to agree with the experimental results. The compounds 4g and 4h showed the best affinities toward protein, with a binding energy value of -6.8 kcal/mol.

Recent Development on Sensing Strategies for Small Molecules Detections.

Sensors play a critical role in the detection and monitoring of various substances present in our environment, providing us with valuable information about the world around us. Within the field of sensor development, one area that holds particular importance is the detection of small molecules. Small molecules encompass a wide range of organic or inorganic compounds with low molecular weight, typically below 900 Daltons including gases, volatile organic compounds, solvents, pesticides, drugs, biomarkers, toxins, and pollutants. The accurate and efficient detection of these small molecules has attracted significant interest from the scientific community due to its relevance in diverse fields such as environmental pollutants monitoring, medical diagnostics, industrial optimization, healthcare remedies, food safety, ecosystems, and aquatic and terrestrial life preservation. To meet the demand for precise and efficient monitoring of small molecules, this summary aims to provide an overview of recent advancements in sensing and quantification strategies for various organic small molecules including Hydrazine, Glucose, Morpholine, Ethanol amine, Nitrosamine, Oxygen, Nitro-aromatics, Phospholipids, Carbohydrates, Antibiotics, Pesticides, Drugs, Adenosine Triphosphate, Aromatic Amine, Glutathione, Hydrogen Peroxide, Acetone, Methyl Parathion, and Thiophenol. The focus is on understanding the receptor sensing mechanism, along with the electrical, optical, and electrochemical response. Additionally, the variations in UV-visible spectral properties of the ligands upon treatment with the receptor, fluorescence and absorption titration analysis for limit of detection (LOD) determination, and bioimaging analysis are discussed wherever applicable. It is anticipated that the information gathered from this literature survey will be helpful for the perusal of innovation regarding sensing strategies.

γ-Glutamyltranspeptidase (GGT) Sensitive Fluorescence Probes for Cancer Diagnosis; Brief Review.

Millions of deaths occur each year due to the late diagnosis of abnormal cellular growth within the body. However, the devastating impact of this can be significantly reduced if cancer metastasis is detected early through the use of enzymatic biomarkers. Among several biomarkers, γ-glutamyltranspeptidase (GGT) stands out as a member of the aminopeptidase family. It is primarily found on the surface of cancer cells such as glioma, ovarian, lung, and prostate cancer, without being overexpressed in normal cells or tissues. Recent years have witnessed significant progress in the field of cancer monitoring and imaging. Fluorescence sensing techniques have been employed, utilizing organic small molecular probes with enzyme-specific recognition sites. These probes emit a fluorescent signal upon interacting with GGT, enabling the imaging, identification, and differentiation of normal and cancerous cells, tissues, and organs. This review article presents a concise overview of recent progress in fluorescent probes developed for the selective detection of GGT, focusing on their applications in cancer imaging. It highlights the observed alterations in the fluorescence and absorption spectra of the probes before and after interaction with GGT. Additionally, the study investigates the changes in the probe molecule's structure following enzyme treatment, evaluates the sensor's detection limit, and consolidated imaging studies conducted using confocal fluorescence analysis. This comprehensive survey is expected to contribute to the advancement of sensing techniques for biomarker detection and cancer imaging, providing valuable insights for refining methodologies and inspiring future developments in this field.

A comparative study on various cell sources for constructing tissue-engineered meniscus.

Injury to the meniscus is a common occurrence in the knee joint and its management remains a significant challenge in the clinic. Appropriate cell source is essential to cell-based tissue regeneration and cell therapy. Herein, three commonly used cell sources, namely, bone marrow mesenchymal stem cell (BMSC), adipose-derived stem cell (ADSC), and articular chondrocyte, were comparatively evaluated to determine their potential for engineered meniscus tissue in the absence of growth factor stimulus. Cells were seeded on electrospun nanofiber yarn scaffolds that share similar aligned fibrous configurations with native meniscus tissue for constructing meniscus tissue in vitro. Our results show that cells proliferated robustly along nanofiber yarns to form organized cell-scaffold constructs, which recapitulate the typical circumferential fiber bundles of native meniscus. Chondrocytes exhibited different proliferative characteristics and formed engineered tissues with distinct biochemical and biomechanical properties compared to BMSC and ADSC. Chondrocytes maintained good chondrogenesis gene expression profiles and produced significantly increased chondrogenic matrix and form mature cartilage-like tissue as revealed by typical cartilage lacunae. In contrast, stem cells underwent predominately fibroblastic differentiation and generated greater collagen, which contributes to improved tensile strengths of cell-scaffold constructs in comparison to the chondrocyte. ADSC showed greater proliferative activity and increased collagen production than BMSC. These findings indicate that chondrocytes are superior to stem cells for constructing chondrogenic tissues while the latter is feasible to form fibroblastic tissue. Combination of chondrocytes and stem cells might be a possible solution to construct fibrocartilage tissue and meniscus repair and regeneration.

Heterologous boost with mRNA vaccines against SARS-CoV-2 Delta/Omicron variants following an inactivated whole-virus vaccine.

The coronavirus SARS-CoV-2 has mutated quickly and caused significant global damage. This study characterizes two mRNA vaccines ZSVG-02 (Delta) and ZSVG-02-O (Omicron BA.1), and associating heterologous prime-boost strategy following the prime of a most widely administrated inactivated whole-virus vaccine (BBIBP-CorV). The ZSVG-02-O induces neutralizing antibodies that effectively cross-react with Omicron subvariants. In naïve animals, ZSVG-02 or ZSVG-02-O induce humoral responses skewed to the vaccine's targeting strains, but cellular immune responses cross-react to all variants of concern (VOCs) tested. Following heterologous prime-boost regimes, animals present comparable neutralizing antibody levels and superior protection against Delta and Omicron BA.1variants. Single-boost only generated ancestral and omicron dual-responsive antibodies, probably by "recall" and "reshape" the prime immunity. New Omicron-specific antibody populations, however, appeared only following the second boost with ZSVG-02-O. Overall, our results support a heterologous boost with ZSVG-02-O, providing the best protection against current VOCs in inactivated virus vaccine-primed populations.

Evaluating Zn-Porphyrin-Based Near-IR-Sensitive Non-Fullerene Acceptors for Efficient Panchromatic Organic Solar Cells.

Porphyrin-based non-fullerene acceptors (NFAs) have shown pronounced potential for assembling low-bandgap materials with near-infrared (NIR) characteristics. Herein, panchromatic-type porphyrin-based molecules (POR1-POR5) are proposed by modulating end-capped acceptors of a highly efficient porphyrin-based NFA PORTFIC(POR) for organic solar cells (OSCs). Quantum chemical structure-property relationship has been studied to discover photovoltaic and optoelectronic characteristics of POR1-POR5. Results show that optoelectronic properties of the POR1-POR5 are better in all aspects when compared with the reference POR. All proposed NFAs particularly POR5 proved to be the preferable porphyrin-based NIR sensitive NFA for OSCs applications owing to lower energy gap (1.56 eV), transition energy (1.11 eV), binding energy (Eb =0.986 eV), electron mobility (λe =0.007013Eh ), hole mobility (λh =0.004686 Eh ), high λmax =1116.27 nm and open-circuit voltage (Voc =1.96 V) values in contrast to the reference POR and other proposed NFAs. This quantum chemical insight provides sufficient evidence about excellent potential of the proposed porphyrin-based NIR sensitive NFA derivatives for their use in OSCs.

The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes.

Riboswitches are regulatory noncoding RNAs found in bacteria, fungi and plants, that modulate gene expressions through structural changes in response to ligand binding. Understanding how ligands interact with riboswitches in solution can shed light on the molecular mechanisms of this ancient regulators. Previous studies showed that riboswitches undergo global conformation changes in response to ligand binding to relay information. Here, we report conformation switching models of the recently discovered tetrahydrofolic acid-responsive second class of tetrahydrofolate (THF-II) riboswitches in response to ligand binding. Using a combination of selective 2'-hydroxyl acylation, analyzed by primer extension (SHAPE) assay, 3D modeling and small-angle X-ray scattering (SAXS), we found that the ligand specifically recognizes and reshapes the THF-II riboswitch loop regions, but does not affect the stability of the P3 helix. Our results show that the THF-II riboswitch undergoes only local conformation changes in response to ligand binding, rearranging the Loop1-P3-Loop2 region and rotating Loop1 from a ~120° angle to a ~75° angle. This distinct conformation changes suggest a unique regulatory mechanism of the THF-II riboswitch, previously unseen in other riboswitches. Our findings may contribute to the fields of RNA sensors and drug design.

Lignocellulose Extraction from Sisal Fiber and Its Use in Green Emulsions: A Novel Method.

Regenerated lignocellulose nanofibrils (RLCNFs) have recently piqued the interest of researchers due to their widespread availability and ease of extraction. After dewaxing, we treated sisal fiber with alkali, followed by heating and agitation, to obtain RLCNFs, which were then vacuum oven-dried. We used a variety of characterization techniques, including XRD, SEM, and FT-IR, to assess the effects of the alkali treatment on the sisal fiber. Various characterizations demonstrate that lignocellulose fibrils have been successfully regenerated and contaminants have been removed. In addition, employing the RLCNFs as a stabilizer, stable Pickering emulsions were created. The effects of RLCNF concentration in the aqueous phase and water-to-oil volume ratio on stability were studied. The RLCNFs that have been produced show promise as a stabilizer in Pickering emulsions.

Novel Carboxylic Acid-Capped Silver Nanoparticles as Antimicrobial and Colorimetric Sensing Agents.

The present work reports the synthesis, characterization, and antimicrobial activities of adipic acid-capped silver nanoparticles (AgNPs@AA) and their utilization for selective detection of Hg2+ ions in an aqueous solution. The AgNPs were synthesized by the reduction of Ag+ ions with NaBH4 followed by capping with adipic acid. Characterization of as-synthesized AgNPs@AA was carried out by different techniques, including UV-Visible spectroscopy, Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), X-ray diffraction (XRD), Dynamic Light Scattering (DLS), and zeta potential (ZP). In the UV-Vis absorption spectrum, the characteristic absorption band for AgNPs was observed at 404 nm. The hydrodynamic size of as-synthesized AgNPs was found to be 30 ± 5.0 nm. ZP values (-35.5 ± 2.4 mV) showed that NPs possessed a negative charge due to carboxylate ions and were electrostatically stabilized. The AgNPs show potential antimicrobial activity against clinically isolated pathogens. These AgNPs were found to be selectively interacting with Hg2+ in an aqueous solution at various concentrations. A calibration curve was constructed by plotting concentration as abscissa and absorbance ratio (AControl - AHg/AControl) as ordinate. The linear range and limit of detection (LOD) of Hg2+ were 0.6-1.6 µM and 0.12 µM, respectively. A rapid response time of 4 min was found for the detection of Hg2+ by the nano-probe. The effect of pH and temperature on the detection of Hg2+ was also investigated. The nano-probe was successfully applied for the detection of Hg2+ from tap and river water.

Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World.

The SARS CoV-2 pandemic has affected millions of people around the globe. Despite many efforts to find some effective medicines against SARS CoV-2, no established therapeutics are available yet. The use of phytochemicals as antiviral agents provides hope against the proliferation of SARS-CoV-2. Several natural compounds were analyzed by virtual screening against six SARS CoV-2 protein targets using molecular docking simulations in the present study. More than a hundred plant-derived secondary metabolites have been docked, including alkaloids, flavonoids, coumarins, and steroids. SARS CoV-2 protein targets include Main protease (MPro), Papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), Spike glycoprotein (S), Helicase (Nsp13), and E-Channel protein. Phytochemicals were evaluated by molecular docking, and MD simulations were performed using the YASARA structure using a modified genetic algorithm and AMBER03 force field. Binding energies and dissociation constants allowed the identification of potentially active compounds. Ligand-protein interactions provide an insight into the mechanism and potential of identified compounds. Glycyrrhizin and its metabolite 18-ß-glycyrrhetinic acid have shown a strong binding affinity for MPro, helicase, RdRp, spike, and E-channel proteins, while a flavonoid Baicalin also strongly binds against PLpro and RdRp. The use of identified phytochemicals may help to speed up the drug development and provide natural protection against SARS-CoV-2.

Using tRNA Scaffold to Assist RNA Crystallization.

Recent studies have solidified RNA's regulatory and catalytic roles in all life forms. Understanding such functions necessarily requires high-resolution understanding of the molecular structure of RNA. Whereas proteins tend to fold into a globular structure and gain most of the folding energy from tertiary interactions, RNAs behave the opposite. Their tertiary structure tends to be irregular and porous, and they gain the majority of their folding free energy from secondary structure formation. These properties lead to higher conformational dynamics in RNA structure. As a result, structure determination proves more difficult for RNA using X-ray crystallography and other structural biology tools. Despite the painstaking effort to obtain large quantities of chemically pure RNA molecules, many still fail to crystallize due to the presence of conformational impurity. To overcome the challenge, we developed a new method to crystallize the RNA of interest as a tRNA chimera. In most cases, tRNA fusion significantly increased the conformational purity of our RNA target, improved the success rate of obtaining RNA crystals, and made the subsequent structure determination process much easier. Here in this chapter we describe our protocol to design, stabilize, express, and purify an RNA target as a tRNA chimera. While this method continues a series of work utilizing well-behaving macromolecules/motifs as "crystallization tags" (Ke and Wolberger. Protein Sci 12:306-312, 2003; Ferre-D'Amare and Doudna. J Mol Biol 295:541-556, 2000; Koldobskaya et al . Nat Struct Mol Biol 18:100-106, 2011; Ferre-D'Amare et al. J Mol Biol 279:621-631, 1998), it was inspired by the work of Ponchon and Dardel to utilize tRNA scaffold to express, stabilize, and purify RNA of interest in vivo (Ponchon and Dardel. Nat Methods 4:571-576, 2007). The "tRNA scaffold," where the target RNA is inserted into a normal tRNA, replacing the anticodon sequence, can effectively help the RNA fold, express in various sources and even assist crystallization and phase determination. This approach applies to any generic RNA whose 5' and 3' ends join and form a helix.

Key Electronic, Linear and Nonlinear Optical Properties of Designed Disubstituted Quinoline with Carbazole Compounds.

Organic materials development, especially in terms of nonlinear optical (NLO) performance, has become progressively more significant owing to their rising and promising applications in potential photonic devices. Organic moieties such as carbazole and quinoline play a vital role in charge transfer applications in optoelectronics. This study reports and characterizes the donor-acceptor-donor-π-acceptor (D-A-D-π-A) configured novel designed compounds, namely, Q3D1-Q3D3, Q4D1-Q1D2, and Q5D1. We further analyze the structure-property relationship between the quinoline-carbazole compounds for which density functional theory (DFT) and time-dependent DFT (TDDFT) calculations were performed at the B3LYP/6-311G(d,p) level to obtain the optimized geometries, natural bonding orbital (NBO), NLO analysis, electronic properties, and absorption spectra of all mentioned compounds. The computed values of λmax, 364, 360, and 361 nm for Q3, Q4, and Q5 show good agreement of their experimental values: 349, 347, and 323 nm, respectively. The designed compounds (Q3D1-Q5D1) exhibited a smaller energy gap with a maximum redshift than the reference molecules (Q3-Q5), which govern their promising NLO behavior. The NBO evaluation revealed that the extended hyperconjugation stabilizes these systems and caused a promising NLO response. The dipole polarizabilities and hyperpolarizability (ß) values of Q3D1-Q3D3, Q4D1-Q1D2, and Q5D1 exceed those of the reference Q3, Q4, and Q5 molecules. These data suggest that the NLO active compounds, Q3D1-Q3D3, Q4D1-Q1D2, and Q5D1, may find their place in future hi-tech optical devices.

Cell membrane camouflaged bismuth nanoparticles for targeted photothermal therapy of homotypic tumors.

Bi nanoparticles (NPs) have been demonstrated as effective all-in-one type theranostic agent for imaging-guided photothermal therapy, but their applications have been limited by relatively low biocompatibility and target accumulation capacity. To address this issue, we report the camouflage of Bi NPs (size: ~42 ± 2 nm) by using the mouse colon cancer CT26 cells membrane (CT26 CCM). The camouflaging process confers the efficient coating of CCM shell layer with thickness of ~8 ± 2 nm on Bi NPs cores, which can be confirmed by TEM image, zeta potential and protein gel electrophoresis tests. Simultaneously, CCM shell has no side effects on the photoabsorption/photothermal effect. Importantly, Bi@CCM NPs retain significant features of CCM, including good biocompatibility and homologous targeting ability. When Bi@CCM dispersion was intravenously (i.v.) injected into mice, they exhibited higher blood circulation half-life (11.5 h, ~2.9 times) and accumulation amount (4.7 ± 0.56% ID/g, ~2.3 times) in homotypic CT26 tumor compared to those (4.0 h in blood and 2.03 ± 0.60% ID/g in tumor) from uncoated Bi NPs. After 808 nm laser irradiation, CT26 cancer cells could be effectively ablated after the photothermal therapy of high-accumulated Bi@CCM NPs, and then the tumor tends to be eradicated after 12 days. Thus, Bi NPs camouflaged with CT26 CCM have great potential for the targeted photothermal therapy of homotypic tumors.

Aspirin Repurposing in Folate-Decorated Nanoparticles: Another Way to Target Breast Cancer.

Breast cancer affects more than 1 million women per year worldwide. Through this study, we developed a nanoparticle-based drug delivery system to target breast cancer cells. Aspirin has been found to inhibit thromboembolic diseases with its tumor-preventing activity. As a consequence, it relieves disease symptoms and severity. Here, mesoporous silica nanoparticles (MNPs) have been used to deliver aspirin to the tumor location. MNP-based aspirin in folic acid (F)-conjugated polydopamine (MNP-Asp-PD-PG-F) vehicles are prepared for targeted breast cancer therapy. The vehicle hinges on MNP altered with polymer polyethylene glycol (PG), polydopamine (PD), and F. The delivery vehicle was studied for in vitro drug release, cytotoxicity, and breast cancer cell proliferation. F-conjugated drug delivery vehicles let MNPs achieve an elevated targeting efficacy, ideal for cancer therapy. It was also observed that compared to free aspirin, our drug delivery system (MNP-Asp-PD-PG-F) has a higher cytotoxic and antiproliferative effect on breast cancer cells. The drug delivery system can be proposed as a targeted breast cancer therapy that could be further focused on other targeted cancer therapies. Delivering aspirin by the PD-PG-F system on the tumor sites promises a therapeutic potential for breast cancer treatment.

Effect of balanced nutrient fertilizer: A case study in Pinggu District, Beijing, China.

Agriculture has played an indispensable role in the economic and social development of China. However, the inappropriate application of fertilizers in agriculture has brought about environmental pollution. Therefore, under the requirements of green development, the inevitable choice has been reducing the application amount while increasing the utilization rate of fertilizers. To solve the problems resulting from fertilizers, this research designed and made Balanced Nutrient Fertilizer based on the nutrient balance method. To test Balanced Nutrient Fertilizer, continuous planting experiments on three crops (peas, corns, and peaches) were carried out in Pinggu District, Beijing. Furthermore, a substance flow analysis (SFA) was conducted to obtain a deeper understanding of the Balanced Nutrient Fertilizer. Through a series of tests, the application of Balanced Nutrient Fertilizer was shown to increase the crop yield by 3%. The product quality was also improved. In addition, the amount of nutrients applied was significantly reduced in the experimental group (specifically, 35%-88% for nitrogen, 69%-93% for phosphorus, and 8%-82% for potassium). The results of the SFA revealed that applying the Balanced Nutrient Fertilizer could meet the required amount of nutrients for the best crop growth, greatly decrease the negative influence of chemical fertilizers on the soil and reduce agricultural non-point source pollution.

Intein-mediated recombinant expression of monomeric B22Asp desB30 insulin.

BACKGROUND: Insulin controls hyperglycemia caused by diabetes, and virtually all treatments require exogenous insulin. However, the product's extensive post-translational modifications have hindered the manufacture of recombinant insulin. RESULT: Here we report a novel production method for a monomeric B22Asp desB30 insulin analog (B22D desB30 insulin). Its precursor, DPIP, is fused to an N-terminal chitin-binding domain and intein self-cleavage tag. The fusion protein is expressed and purified from E. coli and immobilized on chitin resins. DPIP is then released using an optimized pH shift and converted to mature insulin via trypsin digest. The resulting product appears monomeric, > 90% pure and devoid of any exogenous enzyme. CONCLUSION: Thus, biologically active insulin analog can be efficiently produced in bacteria and potentially applicable in the treatment of human diabetes.

ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor.

Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA-gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a 'Z'-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.

A review on native and denaturing purification methods for non-coding RNA (ncRNA).

Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.