A general strategy for engineering GU base pairs to facilitate RNA crystallization.

X-ray crystallography is a fundamental technique that provides atomic-level insights into RNA structures. However, obtaining crystals of RNA structures diffracting to high resolution is challenging. We introduce a simple strategy to enhance the resolution limit of RNA crystals by the selective substitution of Watson-Crick pairs by GU pairs within RNA sequences.

The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.

MTR1 is an in vitro-selected alkyl transferase ribozyme that transfers an alkyl group from -alkylguanine to N1 of the target adenine in the RNA substrate (A63). The structure of the ribozyme suggested a mechanism in which a cytosine (C10) acts as a general acid to protonate -alkylguanine N1. Here, we have analyzed the role of the C10 general acid and the A63 nucleophile by atomic mutagenesis and computation.

Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology.

Nature continually refines its processes for optimal efficiency, especially within biological systems. This article explores the collaborative efforts of researchers worldwide, aiming to mimic nature's efficiency by developing smarter and more effective nanoscale technologies and biomaterials. Recent advancements highlight progress and prospects in leveraging engineered nucleic acids and proteins for specific tasks, drawing inspiration from natural functions.

Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level.

Riboswitches are regulatory elements found in bacterial mRNAs that control downstream gene expression through ligand-induced conformational changes. Here, we used single-molecule FRET to map the conformational landscape of the translational SAM/SAH riboswitch and probe how co-transcriptional ligand-induced conformational changes affect its translation regulation function. Riboswitch folding is highly heterogeneous, suggesting a rugged conformational landscape that allows for sampling of the ligand-bound conformation even in the absence of ligand.

Structure and ion-dependent folding of k-junctions.

k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of and thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the and riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding.

Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.

A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1.

Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets.

We present crystal structures of a new NAD+-binding riboswitch termed NAD+-II, bound to nicotinamide mononucleotide (NMN), nicotinamide adenine dinucleotide (NAD+) and nicotinamide riboside (NR). The RNA structure comprises a number of structural features including three helices, one of which forms a triple helix by interacting with an A5 strand in its minor-groove, and another formed from a long-range pseudoknot. The core of the structure (centrally located and coaxial with the triplex and the pseudoknot) includes two consecutive quadruple base interactions.

Ionocaloric refrigeration cycle.

Developing high-efficiency cooling with safe, low-global warming potential refrigerants is a grand challenge for tackling climate change. Caloric effect-based cooling technologies, such as magneto- or electrocaloric refrigeration, are promising but often require large applied fields for a relatively low coefficient of performance and adiabatic temperature change. We propose using the ionocaloric effect and the accompanying thermodynamic cycle as a caloric-based, all-condensed-phase cooling technology.

Search and processing of Holliday junctions within long DNA by junction-resolving enzymes.

Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction.

Ribocentre: a database of ribozymes.

Ribozymes are excellent systems in which to study 'sequence - structure - function' relationships in RNA molecules. Understanding these relationships may greatly help structural modeling and design of functional RNA structures and some functional structural modules could be repurposed in molecular design. At present, there is no comprehensive database summarising all the natural ribozyme families.

Analysis of the management of ventriculitis cases at a UK neurosurgery centre.

Background: Ventriculitis is an infection of the ventricular system of the central nervous system associated with neurosurgery and/or indwelling medical devices mainly caused by coagulase-negative staphylococci and increasingly by Gram-negative bacilli and other Gram-positive bacteria. The Infectious Diseases Society of America (IDSA) and the neurosurgery department University Hospital Coventry and Warwickshire (UHCW) have treatment guidelines for ventriculitis which recommend antimicrobials and device removal.

Methods: Data on ventriculitis cases, their management and outcomes were collected from electronic laboratory and hospital records as well as patients' paper records from 2009 to 2019.

Methods to stabilize aqueous supercooling identified by use of an isochoric nucleation detection (INDe) device.

Stable aqueous supercooling has shown significant potential as a technique for human tissue preservation, food cold storage, conservation biology, and beyond, but its stochastic nature has made its translation outside the laboratory difficult. In this work, we present an isochoric nucleation detection (INDe) platform for automated, high-throughput characterization of aqueous supercooling at >1 mL volumes, which enables statistically-powerful determination of the temperatures and time periods for which supercooling in a given aqueous system will remain stable. We employ the INDe to investigate the effects of thermodynamic, surface, and chemical parameters on aqueous supercooling, and demonstrate that various simple system modifications can significantly enhance supercooling stability, including isochoric (constant-volume) confinement, hydrophobic container walls, and the addition of even mild concentrations of solute.

Structure and mechanism of a methyltransferase ribozyme.

Known ribozymes in contemporary biology perform a limited range of chemical catalysis, but in vitro selection has generated species that catalyze a broader range of chemistry; yet, there have been few structural and mechanistic studies of selected ribozymes. A ribozyme has recently been selected that can catalyze a site-specific methyl transfer reaction. We have solved the crystal structure of this ribozyme at a resolution of 2.

Thermal fluids with high specific heat capacity through reversible Diels-Alder reactions.

Thermal fluids are used as heat transfer fluids and thermal energy storage media in many energy technologies ranging from solar thermal heating to battery thermal management. The heat capacity of state-of-the-art thermal fluids remains ∼50% of that of water (which suffers from a limited operation range between 0°C and 100°C), and their viscosities are typically more than one order of magnitude higher than that of water. Our results demonstrate that the heat capacity of the proposed thermochemical fluid is significantly higher than that of state-of-the-art thermal fluids over a broad temperature range and is also higher than that of water between 60°C and 90°C.

Protocol for a meta-narrative review on research paradigms addressing the urban built environment and human health.

Background: Urban health is a field of research and practice that has attracted the interest of various disciplines. While it is encouraged for diverse disciplines to contribute to a multidisciplinary field of study such as urban health, this often results in tensions, conflicts or competition between the different traditions that stem from different epistemological backgrounds. This meta-narrative review aims to identify and describe the multiple paradigms and articulate the underlying epistemological, ontological, methodological, and aetiological differences in their approaches.

Hollow Atomic Force Microscopy Cantilevers with Nanoscale Wall Thicknesses.

In atomic force microscopy, the cantilever probe is a critical component whose properties determine the resolution and speed at which images with nanoscale resolution can be obtained. Traditional cantilevers, which have moderate resonant frequencies and high quality factors, have relatively long response times and low bandwidths. In addition, cantilevers can be easily damaged by excessive deformation, and tips can be damaged by wear, requiring them to be replaced frequently.

Myrcene-What Are the Potential Health Benefits of This Flavouring and Aroma Agent?

Myrcene (β-myrcene) is an abundant monoterpene which occurs as a major constituent in many plant species, including hops and cannabis. It is a popular flavouring and aroma agent (food additive) used in the manufacture of food and beverages. This review aims to report on the occurrence, biological and toxicological profile of β-myrcene.

The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome.

The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome.

Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules.

k-Turns are widespread key architectural elements that occur in many classes of RNA molecules. We have shown previously that their folding properties (whether or not they fold into their tightly kinked structure on addition of metal ions) and conformation depend on their local sequence, and we have elucidated a series of rules for prediction of these properties from sequence. In this work, we have expanded the rules for prediction of folding properties, and then applied the full set to predict the folding and conformation of four probable k-turns we have identified amongst 224 structured RNA species found in bacterial intergenenic regions by the Breaker lab (1).

The potential versatility of RNA catalysis.

It is commonly thought that in the early development of life on this planet RNA would have acted both as a store of genetic information and as a catalyst. While a number of RNA enzymes are known in contemporary cells, they are largely confined to phosphoryl transfer reactions, whereas an RNA based metabolism would have required a much greater chemical diversity of catalysis. Here we discuss how RNA might catalyze a wider variety of chemistries, and particularly how information gleaned from riboswitches could suggest how ribozymes might recruit coenzymes to expand their chemical range.