Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding

Understanding the Thermodynamics of Magnesium Binding to RNA Structural Motifs

Divalent magnesium ions (Mg2+) serve a vital role in defining the structural and catalytic chemistry of a wide array of RNA molecules. The body of structural information on RNA motifs continues to expand and, in turn, the functional importance of Mg2+ is revealed. A combination of prior work on the structural characterization of magnesium binding ligands with inner- and outer-sphere coordination modes, with recorded experimental binding energies for inner- and outer-sphere contacts, demonstrates the relative affinity and thermodynamic hierarchy for these sites. In turn, these can be correlated with cellular concentrations of free available magnesium ions, allowing the prioritization of populating important functional sites and a correlation with physiological function. This paper summarizes some of the key results of that analysis and provides predictive rules for the affinity and role of newly identified Mg binding sites on complex RNA structures. The influence of crystal packing on magnesium binding to RNA motifs, relative to their solution form, is addressed and caveats made.

Spectroscopic and Biophysical Methods to Determine Differential Salt-Uptake by Primitive Membraneless Polyester Microdroplets

α-Hydroxy acids are prebiotic monomers that undergo dehydration synthesis to form polyester gels, which assemble into membraneless microdroplets upon aqueous rehydration. These microdroplets are proposed as protocells that can segregate and compartmentalize primitive molecules/reactions. Different primitive aqueous environments with a variety of salts could have hosted chemistries that formed polyester microdroplets. These salts could be essential cofactors of compartmentalized prebiotic reactions or even directly affect protocell structure. However, fully understanding polyester-salt interactions remains elusive, partially due to technical challenges of quantitative measurements in condensed phases. Here, spectroscopic and biophysical methods are applied to analyze salt uptake by polyester microdroplets. Inductively coupled plasma mass spectrometry is applied to measure the cation concentration within polyester microdroplets after addition of chloride salts. Combined with methods to determine the effects of salt uptake on droplet turbidity, size, surface potential and internal water distribution, it was observed that polyester microdroplets can selectively partition salt cations, leading to differential microdroplet coalescence due to ionic screening effects reducing electrostatic repulsion forces between microdroplets. Through applying existing techniques to novel analyses related to primitive compartment chemistry and biophysics, this study suggests that even minor differences in analyte uptake can lead to significant protocellular structural change.

Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering

Engineering in vitro selected RNA aptamers into in vivo functional riboswitches represents a long-standing challenge in molecular biology. The highly specific aptamer domain of the riboswitch undergoes a conformational adjustment in response to ligand sensing, which in turn exerts the regulatory function. Besides essential factors like structural complexity and ligand binding kinetics, the active role of magnesium ions in stabilizing RNA tertiary structures and assisting in ligand binding can be a vital criterion. We present spectroscopic studies on the magnesium ion-driven folding of the Tetracycline binding aptamer. Using fluorescent labels, the aptamer pre-folding and subsequent ligand binding is monitored by magnesium titration experiments and time-resolved stopped-flow measurements. A minimum concentration of 0.5 mM magnesium is required to fold into a magnesium ion-stabilized binding-competent state with a preformed binding pocket. Tetracycline binding causes a pronounced conformational change that results in the establishment of the triple helix core motif, and that further propagates towards the closing stem. By a dynamic acquisition of magnesium ions, a kink motif is formed at the intersection of the triple helix and closing stem regions. This ultimately entails a stabilization of the closing stem which is discussed as a key element in the regulatory function of the Tetracycline aptamer.

Cation-dependent assembly of hexagonal DNA origami lattices on SiO2 surfaces

DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.

Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch

The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) predicted over 10 inner-shell Mg2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminishes the selectivity between SAM and SAH. One Mg2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg2+ thus plays vital roles in SAM/SAH riboswitch function.

Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch

The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg 2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) identified over 10 inner-shell Mg 2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminish the selectivity between SAM and SAH. One Mg 2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg 2+ thus plays vital roles in SAM/SAH riboswitch function.

How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active

The modern ribosome catalyzes all coded protein synthesis in extant organisms. It is likely that its core structure is a direct descendant from the ribosome present in the last common ancestor (LCA). Hence, its earliest origins likely predate the LCA and therefore date further back in time. Of special interest is the pseudosymmetrical region (SymR) that lies deep within the large subunit (LSU) where the peptidyl transfer reaction takes place. It was previously proposed that two RNA oligomers, representing the P- and A-regions of extant ribosomes dimerized to create a pore-like structure, which hosted the necessary properties that facilitate peptide bond formation. However, recent experimental studies show that this may not be the case. Instead, several RNA constructs derived exclusively from the P-region were shown to form a homodimer capable of peptide bond synthesis. Of special interest will be the origin issues because the homodimer would have allowed a pre-LCA ribosome that was significantly smaller than previously proposed. For the A-region, the immediate issue will likely be its origin and whether it enhances ribosome performance. Here, we reanalyze the RNA/RNA interaction regions that most likely lead to SymR formation in light of these recent findings. Further, it has been suggested that the ability of these RNA constructs to dimerize and enhance peptide bond formation is sequence-dependent. We have analyzed the implications of sequence variations as parts of functional and nonfunctional constructs.

Structural Studies Reveal that Endosomal Cations Promote Formation of Infectious Coxsackievirus A9 A-Particles, Facilitating RNA and VP4 Release

Coxsackievirus A9 (CVA9), an enterovirus, is a common cause of pediatric aseptic meningitis and neonatal sepsis. During cell entry, enterovirus capsids undergo conformational changes leading to expansion, formation of large pores, externalization of VP1 N termini, and loss of the lipid factor from VP1. Factors such as receptor binding, heat, and acidic pH can trigger capsid expansion in some enteroviruses. Here, we show that fatty acid-free bovine serum albumin or neutral endosomal ionic conditions can independently prime CVA9 for expansion and genome release. Our results showed that CVA9 treatment with albumin or endosomal ions generated a heterogeneous population of virions, which could be physically separated by asymmetric flow field flow fractionation and computationally by cryo-electron microscopy (cryo-EM) and image processing. We report cryo-EM structures of CVA9 A-particles obtained by albumin or endosomal ion treatment and a control nonexpanded virion to 3.5, 3.3, and 2.9 Å resolution, respectively. Whereas albumin promoted stable expanded virions, the endosomal ionic concentrations induced unstable CVA9 virions which easily disintegrated, losing their genome. Loss of most of the VP4 molecules and exposure of negatively charged amino acid residues in the capsid's interior after expansion created a repulsive viral RNA-capsid interface, aiding genome release. IMPORTANCE Coxsackievirus A9 (CVA9) is a common cause of meningitis and neonatal sepsis. The triggers and mode of action of RNA release into the cell unusually do not require receptor interaction. Rather, a slow process in the endosome, independent of low pH, is required. Here, we show by biophysical separation, cryogenic electron microscopy, and image reconstruction that albumin and buffers mimicking the endosomal ion composition can separately and together expand and prime CVA9 for uncoating. Furthermore, we show in these expanded particles that VP4 is present at only ~10% of the occupancy found in the virion, VP1 is externalized, and the genome is repelled by the negatively charged, repulsive inner surface of the capsid that occurs due to the expansion. Thus, we can now link observations from cell biology of infection with the physical processes that occur in the capsid to promote genome uncoating.

Coordination of Phosphate and Magnesium Metabolism in Bacteria

The majority of cellular phosphate (PO₄^-3; Pi) exists as nucleoside triphosphates, mainly adenosine triphosphate (ATP), and ribosomal RNA (rRNA). ATP and rRNA are also the largest cytoplasmic reservoirs of magnesium (Mg²⁺), the most abundant divalent cation in living cells. The co-occurrence of these ionic species in the cytoplasm is not coincidental. Decades of work in the Pi and Mg²⁺ starvation responses of two model enteric bacteria, Escherichia coli and Salmonella enterica, have led to the realization that the metabolisms of Pi and Mg²⁺ are interconnected. Bacteria must acquire these nutrients in a coordinated manner to achieve balanced growth and avoid loss of viability. In this chapter, we will review how bacteria sense and respond to fluctuations in environmental and intracellular Pi and Mg²⁺ levels. We will also discuss how these two compounds are functionally linked, and how cells elicit physiological responses to maintain their homeostasis.

In vitro evolution reveals non-cationic protein-RNA interaction mediated by metal ions

RNA–peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA–protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 10¹⁰ library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K⁺/Mg²⁺) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein–RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules

Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.

Structure and Mechanical Stabilities of the Three-Way Junction Motifs in Prohead RNA

The core structure of phi29 prohead RNA (pRNA) is composed of three major helices organized into three-way junction pRNA (3WJ-pRNA) and has stout structural rigidity along the coaxial helices. Prohead RNAs of the other Bacillus subtilis bacteriophages such as GA1 and SF5 share similar secondary structure and function with phi29; whether these pRNAs have similar mechanical rigidity remains to be elucidated. In this study, we constructed the tertiary structures of GA1 and SF5 3WJ-pRNAs by comparative modeling. Both GA1 and SF5 3WJ-pRNAs adopt a similar structure, in which three helices are organized as the three-way junction and two of the three helices are stacked coaxially. Moreover, detailed structural features of GA1 and SF5 3WJ-pRNAs are also similar to those of phi29 3WJ-pRNA: all of the bases of the coaxial helices are paired, and all of the adenines in the junction region are paired, which eliminates the interference of A-minor tertiary interactions. Hence, the coaxial helices tightly join to each other, and the major groove between them is very narrow. Two Mg²⁺ ions can thus fit into this major groove and form double Mg clamps. A steered molecular dynamics simulation was used to study the mechanical properties of these 3WJ-pRNAs. Both GA1 and SF5 3WJ-pRNAs show strong resistance to applied force in the direction of their coaxial helices. Such mechanical stability can be attributed to the Mg clamps.

Theoretical study on isomerization of α-acids: A DFT calculation

The α-acids contained in hops are one of the ingredients of beer. The isomerization of α-acids produces iso-α-acids, the main source of bitterness in beer. In this study, the isomerization mechanism of the α-acid, cohumulone, was elucidated by using density functional theory in conjunction with the polarizable continuum model or 3D-RISM integral equation theory of liquids. The calculated reaction diagram is consistent with experimental results; the activation free energy difference between the cis and trans isomers is in good agreement with the experimental estimate. The activation energy difference results from solvation energy. Additionally, a calculation of NMR chemical shifts showed that the proton position of isocohumulone is different from that proposed previously. The effect of Mg²⁺ cation on the isomerization was also investigated. Both the activation and reaction free energy are stabilized by the presence of Mg²⁺, which is consistent with experimental results. Water solvation reduces the activation free energy.

Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules-Preliminary validations of a polarizable potential by ab initio quantum chemistry

Dimethyl phosphate (DMP^- ) is a model for the phosphodiester backbone of DNA, RNA, and phospholipids. It is central for the binding of divalent cations and water along the backbone of nucleic acids. Significant polarization and charge-transfer contributions and nonadditivity come into play in the multimolecular complexes organized around phosphate. Prior to large-scale molecular dynamics (MD) with advanced polarizable potentials, it is essential to evaluate how well the values and trends of intermolecular interaction energies (ΔE) from ab initio quantum chemistry (QC) and their individual contributions are reproduced in a diversity of such complexes. These differ by the starting binding modes of a divalent cation, Zn(II), namely direct, bi- or mono-dentate to anionic and/or ester oxygens, versus through-water binding. We present first the results from automated refinements of the individual contributions of the SIBFA potential with respect to their QC counterparts using a Zn(II) or a water probe. This is followed by validations on eight relaxed multimolecular complexes of DMP^- with Zn(II) or Mg(II) and seven waters, then on sixteen complexes of DMP^- with Zn(II) and eight waters in arrangements extracted from MD or energy-minimization on a droplet of sixty-four waters. This monitors the compared evolutions of SIBFA and QC ΔE and their individual contributions in the competing arrangements. Some waters, bridging Zn(II) and DMP^- , were found to have exceptionally large dipole moments, of up to 3.8 Debye. The perspectives of extension to a flexible phosphodiester backbone are discussed in the context of the SIBFA potential for DNA and RNA.

Metal Affinity/Selectivity of Monophosphate-Containing Signaling/Lipid Molecules

Monophosphate, an essential component of nucleic acids, as well as cell membranes and signaling molecules, is often bound to metal cations. Despite the biological importance of monophosphate-containing cell-signaling or lipid molecules, their propensity to bind the two most abundant cellular dications, Mg²⁺ and Ca²⁺, in a particular mode (inner/outer shell, mono/bidentate) is not well understood. Whether they prefer binding to Mg²⁺ than to Ca²⁺ and if they can outcompete the carboxylates of excitatory Asp/Glu and inhibitory gamma-aminobutyric acid (GABA) neurotransmitters in binding to Mg²⁺/Ca²⁺ remain unclear. To address these questions, we modeled cyclic adenosine/guanosine monophosphate (cAMP/cGMP), nucleoside 2',3'-cyclic phosphate, phosphatidylinositol (PI), phosphatidylserine (PS), and phosphatidylethanolamine (PEA) and determined their most stable metal-binding modes, including those of Asp/Glu and GABA, as well as their selectivity for Mg²⁺/Ca²⁺ using density functional theory combined with the polarizable continuum model. The results obtained, which are consistent with the available experimental findings, reveal that the structurally and functionally diverse monophosphate-containing ligands studied prefer monodentate coordination of Mg²⁺ because of the greater strain encountered upon bidentate coordination, whereas the larger Ca²⁺ imposes less strain upon bidentate binding and has reduced/no preference for monodentate coordination. We further show that in a low-dielectric environment, negatively charged monophosphate-containing ligands favor the better charge-accepting dication, that is, Mg²⁺ rather than Ca²⁺. By promoting Mg²⁺ over Ca²⁺ binding, signaling monophosphates (cAMP/cGMP) do not entrap cellular Ca²⁺ and interfere with signal transduction processes employing Ca²⁺ as a second messenger. In regions with high glutamate cytoplasmic concentration, glutamate may sequester Mg²⁺ bound to isolated five-/six-membered ring phosphates, PI, or neutral PEA, but not anionic phospholipids constituting the inner leaflet of the cell membrane.

Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations

Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the molecular level. Here, we demonstrate that contact ion pairs of magnesium (Mg²⁺) and phosphate groups embedded in local water shells stabilize the tertiary equilibrium structure of transfer RNA (tRNA). Employing dialyzed tRNA^Phe from yeast and tRNA from Escherichia coli, we follow the population of Mg²⁺ sites close to phosphate groups of the ribose-phosphodiester backbone step by step, combining linear and nonlinear infrared spectroscopy of phosphate vibrations with molecular dynamics simulations and ab initio vibrational frequency calculations. The formation of up to six Mg²⁺/phosphate contact pairs per tRNA and local field-induced reorientations of water molecules balance the phosphate–phosphate repulsion in nonhelical parts of tRNA, thus stabilizing the folded structure electrostatically. Such geometries display limited sub-picosecond fluctuations in the arrangement of water molecules and ion residence times longer than 1 μs. At higher Mg²⁺ excess, the number of contact ion pairs per tRNA saturates around 6 and weakly interacting ions prevail. Our results suggest a predominance of contact ion pairs over long-range coupling of the ion atmosphere and the biomolecule in defining and stabilizing the tertiary structure of tRNA.

Iron-mediated degradation of ribosomes under oxidative stress is attenuated by manganese

Protein biosynthesis is fundamental to cellular life and requires the efficient functioning of the translational machinery. At the center of this machinery is the ribosome, a ribonucleoprotein complex that depends heavily on Mg2+ for structure. Recent work has indicated that other metal cations can substitute for Mg2+, raising questions about the role different metals may play in the maintenance of the ribosome under oxidative stress conditions. Here, we assess ribosomal integrity following oxidative stress both in vitro and in cells to elucidate details of the interactions between Fe2+ and the ribosome and identify Mn2+ as a factor capable of attenuating oxidant-induced Fe2+-mediated degradation of rRNA. We report that Fe2+ promotes degradation of all rRNA species of the yeast ribosome and that it is bound directly to RNA molecules. Furthermore, we demonstrate that Mn2+ competes with Fe2+ for rRNA-binding sites and that protection of ribosomes from Fe2+-mediated rRNA hydrolysis correlates with the restoration of cell viability. Our data, therefore, suggest a relationship between these two transition metals in controlling ribosome stability under oxidative stress.

Graphene Oxide Nano-Concentrators Selectively Modulate RNA Trapping According to Metal Cations in Solution

With recent advances in nanotechnology, graphene nanomaterials are being translated to applications in the fields of biosensing, medicine, and diagnostics, with unprecedented power. Graphene is a carbon allotrope derived from graphite exfoliation made of an extremely thin honeycomb of sp2 hybridized carbons. In comparison with the bulk materials, graphene and its water-soluble derivative graphene oxide have a smaller size suitable for diagnostic platform miniaturization as well as high surface area and consequently loading of a large number of biological probes. In this work, we propose a nanotechnological method for concentrating total RNA solution and/or enriching small RNA molecules. To this aim, we exploited the unique trapping effects of GO nanoflakes in the presence of divalent cations (i.e., calcium and magnesium) that make it flocculate and precipitate, forming complex meshes that are positively charged. Here, we demonstrated that GO traps can concentrate nucleic acids in the presence of divalent cations and that small RNAs can be selectively released from GO-magnesium traps. GO nano-concentrators will allow better analytical performance with samples available in small amounts and will increase the sensitivity of sequencing platforms by short RNA selection.

Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in RNA

Divalent cations are often required to fold RNA, which is a highly charged polyanion. Condensation of ions, such as Mg²⁺ or Ca²⁺, in the vicinity of RNA renormalizes the effective charges on the phosphate groups, thus minimizing the intra RNA electrostatic repulsion. The prevailing view is that divalent ions bind diffusively in a nonspecific manner. In sharp contrast, we arrive at the exact opposite conclusion using a theory for the interaction of ions with the phosphate groups using RISM theory in conjunction with simulations based on an accurate three-interaction-site RNA model. The divalent ions bind in a nucleotide-specific manner using either the inner (partially dehydrated) or outer (fully hydrated) shell coordination. The high charge density Mg²⁺ ion has a preference to bind to the outer shell, whereas the opposite is the case for Ca²⁺. Surprisingly, we find that bridging interactions, involving ions that are coordinated to two or more phosphate groups, play a crucial role in maintaining the integrity of the folded state. Their importance could become increasingly prominent as the size of the RNA increases. Because the modes of interaction of divalent ions with DNA are likely to be similar, we propose that specific inner and outer shell coordination could play a role in DNA condensation, and perhaps genome organization as well.

Mg2+ Impacts the Twister Ribozyme through Push-Pull Stabilization of Nonsequential Phosphate Pairs

RNA molecules perform a variety of biological functions for which the correct three-dimensional structure is essential, including as ribozymes where they catalyze chemical reactions. Metal ions, especially Mg2+, neutralize these negatively charged nucleic acids and specifically stabilize RNA tertiary structures as well as impact the folding landscape of RNAs as they assume their tertiary structures. Specific binding sites of Mg2+ in folded conformations of RNA have been studied extensively; however, the full range of interactions of the ion with compact intermediates and unfolded states of RNA is challenging to investigate, and the atomic details of the mechanism by which the ion facilitates tertiary structure formation is not fully known. Here, umbrella sampling combined with oscillating chemical potential Grand Canonical Monte Carlo/molecular dynamics simulations are used to capture the energetics and atomic-level details of Mg2+-RNA interactions that occur along an unfolding pathway of the Twister ribozyme. The free energy profiles reveal stabilization of partially unfolded states by Mg2+, as observed in unfolding experiments, with this stabilization being due to increased sampling of simultaneous interactions of Mg2+ with two or more nonsequential phosphate groups. Notably, these results indicate a push-pull mechanism in which the Mg2+-RNA interactions actually lead to destabilization of specific nonsequential phosphate-phosphate interactions (i.e., pushed apart), whereas other interactions are stabilized (i.e., pulled together), a balance that stabilizes unfolded states and facilitates the folding of Twister, including the formation of hydrogen bonds associated with the tertiary structure. This study establishes a better understanding of how Mg2+-ion interactions contribute to RNA structural properties and stability.

Compositional heterogeneity confers selective advantage to model protocellular membranes during the origins of cellular life

Protocellular membranes are thought to be composed of mixtures of single chain amphiphiles, such as fatty acids and their derivatives, moieties that would have been part of the complex prebiotic chemical landscape. The composition and physico-chemical properties of these prebiological membranes would have been significantly affected and regulated by their environment. In this study, pertinent properties were systematically characterized, under early Earth conditions. Two different fatty acids were mixed with their respective alcohol and/or glycerol monoester derivatives to generate combinations of binary and tertiary membrane systems. Their properties were then evaluated as a function of multiple factors including their stability under varying pH, varying Mg²⁺ ion concentrations, dilution regimes, and their permeability to calcein. Our results demonstrate how environmental constraints would have acted as important prebiotic selection pressures to shape the evolution of prebiological membranes. The study also illustrates that compositionally diverse membrane systems are more stable and robust to multiple selection pressures, thereby making them more suitable for supporting protocellular life.

Protocells programmed through artificial reaction networks

As the smallest unit of life, cells attract interest due to their structural complexity and functional reliability. Protocells assembled by inanimate components are created as an artificial entity to mimic the structure and some essential properties of a natural cell, and artificial reaction networks are used to program the functions of protocells. Although the bottom-up construction of a protocell that can be considered truly ‘alive’ is still an ambitious goal, these man-made constructs with a certain degree of ‘liveness’ can offer effective tools to understand fundamental processes of cellular life, and have paved the new way for bionic applications. In this review, we highlight both the milestones and recent progress of protocells programmed by artificial reaction networks, including genetic circuits, enzyme-assisted non-genetic circuits, prebiotic mimicking reaction networks, and DNA dynamic circuits. Challenges and opportunities have also been discussed.

In this review, the milestones and recent progress of protocells programmed by various types of artificial reaction networks are highlighted.

New opportunities for designing effective small interfering RNAs

Small interfering RNAs (siRNAs) that silence genes of infectious diseases are potentially potent drugs. A continuing obstacle for siRNA-based drugs is how to improve their efficacy for adequate dosage. To overcome this obstacle, the interactions of antiviral siRNAs, tested in vivo, were computationally examined within the RNA-induced silencing complex (RISC). Thermodynamics data show that a persistent RISC cofactor is significantly more exothermic for effective antiviral siRNAs than their ineffective counterparts. Detailed inspection of viral RNA secondary structures reveals that effective antiviral siRNAs target hairpin or pseudoknot loops. These structures are critical for initial RISC interactions since they partially lack intramolecular complementary base pairing. Importing two temporary RISC cofactors from magnesium-rich hairpins and/or pseudoknots then kickstarts full RNA hybridization and hydrolysis. Current siRNA design guidelines are based on RNA primary sequence data. Herein, the thermodynamics of RISC cofactors and targeting magnesium-rich RNA secondary structures provide additional guidelines for improving siRNA design.

Methods for thermal denaturation studies of nucleic acids in complex with fluorogenic dyes

Thermal denaturation is a common technique in the biophysical study of nucleic acids. These experiments are typically performed by monitoring the increase in absorbance (hyperchromism) of a sample at 260nm with temperature (Mergny & Lacroix, 2003; Puglisi & Tinoco, 1989). This wavelength is chosen as nucleic acids of mixed sequence typically exhibit their maximum absorbance here. Exceptions exist, however, some noncanonical nucleic acid structures exhibit differing spectral changes with temperature, resulting in other wavelengths being convenient reporters of secondary structure. In the case of nucleic acids that bind visible light-absorbing ligands, such as fluorogenic aptamers, another wavelength can be a convenient reporter of secondary structure stability and RNA-ligand recognition. As it can be difficult, if not impossible, to know which wavelength to employ a priori, we have developed a system for obtaining the full UV-visible spectrum of a sample at each wavelength, allowing for the subsequent extraction of the absorbance-temperature profile at the desired wavelength. Here, we describe the apparatus and software used to do so. We also describe another technique for the use of a qPCR instrument for measuring secondary structure stability of fluorescent nucleic acid-ligand complexes.

Competitive Binding of Mg2+ and Na+ Ions to Nucleic Acids: From Helices to Tertiary Structures

Nucleic acids generally reside in cellular aqueous solutions with mixed divalent/monovalent ions, and the competitive binding of divalent and monovalent ions is critical to the structures of nucleic acids because of their polyanionic nature. In this work, we first proposed a general and effective method for simulating a nucleic acid in mixed divalent/monovalent ion solutions with desired bulk ion concentrations via molecular dynamics (MD) simulations and investigated the competitive binding of Mg²⁺/Na⁺ ions to various nucleic acids by all-atom MD simulations. The extensive MD-based examinations show that single MD simulations conducted using the proposed method can yield desired bulk divalent/monovalent ion concentrations for various nucleic acids, including RNA tertiary structures. Our comprehensive analyses show that the global binding of Mg²⁺/Na⁺ to a nucleic acid is mainly dependent on its structure compactness, as well as Mg²⁺/Na⁺ concentrations, rather than the specific structure of the nucleic acid. Specifically, the relative global binding of Mg²⁺ over Na⁺ is stronger for a nucleic acid with higher effective surface charge density and higher relative Mg²⁺/Na⁺ concentrations. Furthermore, the local binding of Mg²⁺/Na⁺ to a phosphate of a nucleic acid mainly depends on the local phosphate density in addition to Mg²⁺/Na⁺ concentrations.

One- and Two-Dimensional High-Resolution NMR from Flat Surfaces

Determining atomic-level characteristics of molecules on two-dimensional surfaces is one of the fundamental challenges in chemistry. High-resolution nuclear magnetic resonance (NMR) could deliver rich structural information, but its application to two-dimensional materials has been prevented by intrinsically low sensitivity. Here we obtain high-resolution one- and two-dimensional ³¹P NMR spectra from as little as 160 picomoles of oligonucleotide functionalities deposited onto silicate glass and sapphire wafers. This is enabled by a factor >10⁵ improvement in sensitivity compared to typical NMR approaches from combining dynamic nuclear polarization methods, multiple-echo acquisition, and optimized sample formulation. We demonstrate that, with this ultrahigh NMR sensitivity, ³¹P NMR can be used to observe DNA bound to miRNA, to sense conformational changes due to ion binding, and to follow photochemical degradation reactions.

Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey

Precise knowledge of Mg²⁺ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg²⁺ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg²⁺ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg²⁺ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg²⁺ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg²⁺ binding sites are fewer than expected since many of those are associated with misidentified Na⁺ or K⁺ We also emphasize that binding of Na⁺ and K⁺ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg²⁺ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg²⁺ stereochemistry is observed, alternative placement of Na⁺, K⁺, or Ca²⁺ must be considered. We also critically examine the use of lanthanides (Yb³⁺, Tb³⁺) as Mg²⁺ substitutes in crystallography experiments.

Phosphate-Magnesium Ion Interactions in Water Probed by Ultrafast Two-Dimensional Infrared Spectroscopy

Electric interactions between ions and ionic molecular groups in aqueous solution play a fundamental role in chemistry and biology. While Mg²⁺ ions are known to strongly affect the structure and folding dynamics of biomolecules, the relevance of different solvation geometries and the underlying interactions are mainly unresolved. We study dynamics and couplings between the hydrated Mg²⁺ and the dimethylphosphate anion, an established model system for the DNA and RNA backbone. The asymmetric (PO₂^-) stretching vibration serves as a sensitive noninvasive probe of phosphate-ion interactions. Femtosecond two-dimensional infrared (2D-IR) spectroscopy directly maps Mg²⁺ ions in contact with the phosphate groups via a distinct blue-shifted signature in the 2D spectrum. Data for different Mg²⁺ concentrations are analyzed by microscopic density functional theory modeling of cluster geometries and associated spectroscopic features, providing spatial assignments of the observed 2D-IR signatures. Phosphate-ion interactions arising from electrostatic Coulomb forces and exchange repulsion are the predominant origin of the observed frequency shifts.

Multiple prebiotic metals mediate translation

Today, Mg2+ is an essential cofactor with diverse structural and functional roles in life's oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, and high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) was used to compare the effect of Mg2+, Fe2+, and Mn2+ on the tertiary structure of rRNA. Then, we used in vitro translation reactions to test whether Fe2+ or Mn2+ could mediate protein production, and quantified ribosomal metal content. We found that (i) Mg2+, Fe2+, and Mn2+ had strikingly similar effects on rRNA folding; (ii) Fe2+ and Mn2+ can replace Mg2+ as the dominant divalent cation during translation of mRNA to functional protein; and (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+ and Mn2+ were abundant, these findings suggest that Fe2+ and Mn2+ played a role in early ribosomal evolution.

Iron-dependent cleavage of ribosomal RNA during oxidative stress in the yeast Saccharomyces cerevisiae

Stress-induced strand breaks in rRNA have been observed in many organisms, but the mechanisms by which they originate are not well-understood. Here we show that a chemical rather than an enzymatic mechanism initiates rRNA cleavages during oxidative stress in yeast (Saccharomyces cerevisiae). We used cells lacking the mitochondrial glutaredoxin Grx5 to demonstrate that oxidant-induced cleavage formation in 25S rRNA correlates with intracellular iron levels. Sequestering free iron by chemical or genetic means decreased the extent of rRNA degradation and relieved the hypersensitivity of grx5Δ cells to the oxidants. Importantly, subjecting purified ribosomes to an in vitro iron/ascorbate reaction precisely recapitulated the 25S rRNA cleavage pattern observed in cells, indicating that redox activity of the ribosome-bound iron is responsible for the strand breaks in the rRNA. In summary, our findings provide evidence that oxidative stress-associated rRNA cleavages can occur through rRNA strand scission by redox-active, ribosome-bound iron that potentially promotes Fenton reaction-induced hydroxyl radical production, implicating intracellular iron as a key determinant of the effects of oxidative stress on ribosomes. We propose that iron binding to specific ribosome elements primes rRNA for cleavages that may play a role in redox-sensitive tuning of the ribosome function in stressed cells.

Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations

The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na+ or Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (ΔG‡ for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.

Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA

Data on the location of alkaline and alkaline earth ions at RNA from crystallography, spectroscopy and computational modeling are reviewed.

Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event

Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis. Results show that Fe2+ can indeed substitute for Mg2+ in catalytic function of these enzymes. Additionally, we use calculations to unravel differences in energetics, structures and reactivities of relevant Mg2+ and Fe2+ complexes. Computation explains why Fe2+ can be a more potent cofactor than Mg2+ in a variety of folding and catalytic functions. We propose that the rise of O2 on Earth drove a Fe2+ to Mg2+ substitution in proteins and nucleic acids, a hypothesis consistent with a general model in which some modern biochemical systems retain latent abilities to revert to primordial Fe2+-based states when exposed to pre-GOE conditions.

Unraveling Mg2+-RNA binding with atomistic molecular dynamics

Interaction with divalent cations is of paramount importance for RNA structural stability and function. We report here a detailed molecular dynamics study of all the possible binding sites for Mg2+ on an RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics, which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases. Based on this, we simulate a carefully chosen set of models that allows us to quantify the effects of competition with monovalent cations, RNA flexibility, and RNA hybridization. Our simulations reproduce the decrease and increase of Mg2+ affinity due to ion competition and hybridization, respectively, and predict that RNA flexibility has a site-dependent effect. This suggests a nontrivial interplay between RNA conformational entropy and divalent cation binding.

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core

U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al. (2014), Nature Struct. Mol. Biol. 21, 544-551]. The structure revealed a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein-RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.

Protein-free ribosomal RNA folds to a near-native state in the presence of Mg2+

The assembled bacterial ribosome contains around 50 proteins and many counterions.

Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

The vital contribution of Mg²⁺ ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg²⁺ exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg²⁺ force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg²⁺ ions in different coordination motifs. As a result, a total of ∼2.5 μs MD simulations (100/200 ns for each run) for two prototypical Mg²⁺-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg²⁺-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg²⁺ ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg²⁺ ion parameters is not in line with the physical origin of the Mg²⁺-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg²⁺ models and provides novel insights for the rational development of next-generation Mg²⁺ FFs to be employed for atomistic simulations of RNA.

Beyond Mg2+: functional interactions between RNA and transition metals

It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg²⁺ to stabilize RNA structures has been emphasized. Recent studies, however, highlight the importance of transition metals in RNA function. Riboswitches that selectively bind Ni²⁺, Co²⁺, and Mn²⁺ have been discovered with specific RNA-metal sites that influence metal-related gene expression. Exogenous metals such as Pt(II) from therapeutics also bind and may inhibit cellular RNA function. Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. These new observations emphasize the importance of transition metals in the field of RNA metallobiochemistry.

Beyond Mg(2+): functional interactions between RNA and transition metals

It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg(2+) to stabilize RNA structures has been emphasized. Recent studies, however, highlight the importance of transition metals in RNA function. Riboswitches that selectively bind Ni(2+), Co(2+), and Mn(2+) have been discovered with specific RNA-metal sites that influence metal-related gene expression. Exogenous metals such as Pt(II) from therapeutics also bind and may inhibit cellular RNA. Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. These new observations emphasize the importance of transition metals in the field of RNA metallobiochemistry.

Collaboration between primitive cell membranes and soluble catalysts

One widely held model of early life suggests primitive cells consisted of simple RNA-based catalysts within lipid compartments. One possible selective advantage conferred by an encapsulated catalyst is stabilization of the compartment, resulting from catalyst-promoted synthesis of key membrane components. Here we show model protocell vesicles containing an encapsulated enzyme that promotes the synthesis of simple fatty acid derivatives become stabilized to Mg²⁺, which is required for ribozyme activity and RNA synthesis. Thus, protocells capable of such catalytic transformations would have enjoyed a selective advantage over other protocells in high Mg²⁺ environments. The synthetic transformation requires both the catalyst and vesicles that solubilize the water-insoluble precursor lipid. We suggest that similar modified lipids could have played a key role in early life, and that primitive lipid membranes and encapsulated catalysts, such as ribozymes, may have acted in conjunction with each other, enabling otherwise-impossible chemical transformations within primordial cells.

Early cells likely consisted of fatty acid vesicles enclosing magnesium-dependent ribozymes. Here, the authors show that fatty acid derivatives can form vesicles that, unlike those formed from only unmodified fatty acids, are stable in the presence of magnesium and could support ribozyme catalysis.

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

The ubiquitous presence of magnesium ions in RNA has long been recognized as a key factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In this work, Mg(2+)-binding architectures in RNA were systematically studied using a database of RNA crystal structures from the Protein Data Bank (PDB). Due to the abundance of poorly modeled or incorrectly identified Mg(2+) ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 'reliable' RNA-bound Mg(2+) sites. The normalized frequencies by which specific RNA atoms coordinate Mg(2+) were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg(2+) sites in RNA structures was designed and applied to the benchmark dataset, yielding a set of 41 types of inner-sphere and 95 types of outer-sphere coordinating patterns. This classification system has also been applied to describe six previously reported Mg(2+)-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg(2+)-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs.

Glasses as sources of condensed phosphates on the early earth

Procedures for the analysis of phosphorus in geological material normally aims for the determination of the total amount of P expressed as orthophosphate [Formula: see text] or the differentiation between inorganic and organic P. This is probably due to analytical difficulties but also to the prevalent opinion that the chemistry of phosphorus in geological environments is almost entirely restricted to the mineral apatite. Because of the low solubility of apatite it is, therefore, commonly argued that little P was around for prebiotic chemistry and that pre-biological processes would essentially have had to do without this indispensable element unless it was provided by alternative sources or mechanisms (such as reduction and activation by lightning or delivery to Earth by celestial bodies). It is a paradox that the potential existence of reactive phosphorus compounds, such as the mineral schreibersite - iron phosphide, in geological material on Earth is seldom considered although we are aware of the existence of such compounds in meteorite material. The content of Al2O3 in rocks appears to be important for the speciation of phosphorus and for how strongly it binds to silicates. In general, low alumina seems to promote the existence of isolated charge-balanced phosphorus complexes.

Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution

The spliceosome is a dynamic assembly of five small nuclear ribonucleoproteins (snRNPs) that removes introns from eukaryotic pre-mRNA. U6 is the most conserved of the spliceosomal snRNAs and participates directly in catalysis. Here, we report the crystal structure of the Saccharomyces cerevisiae U6 snRNP core, containing most of U6 snRNA and all four RRM domains of the Prp24 protein. It reveals a unique interlocked RNP architecture that sequesters the 5′ splice site-binding bases of U6 snRNA. RRMs 1, 2 and 4 of Prp24 form an electropositive groove that binds double-stranded RNA and may nucleate annealing of U4 and U6 snRNAs. Substitutions in Prp24 that suppress a mutation in U6 localize to direct RNA-protein contacts. Our results provide the most complete view to date of a multi-RRM protein bound to RNA, and reveal striking co-evolution of protein and RNA structure.

A novel implicit solvent model for simulating the molecular dynamics of RNA

Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin-Debye model and the Poisson-Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.

Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA

The bacteriophage phi29 DNA packaging motor, one of the strongest biological motors characterized to date, is geared by a packaging RNA (pRNA) ring. When assembled from three RNA fragments, its three-way junction (3WJ) motif is highly thermostable, is resistant to 8 M urea, and remains associated at extremely low concentrations in vitro and in vivo. To elucidate the structural basis for its unusual stability, we solved the crystal structure of this pRNA 3WJ motif at 3.05 Å. The structure revealed two divalent metal ions that coordinate 4 nt of the RNA fragments. Single-molecule fluorescence resonance energy transfer (smFRET) analysis confirmed a structural change of 3WJ upon addition of Mg²⁺. The reported pRNA 3WJ conformation is different from a previously published construct that lacks the metal coordination sites. The phi29 DNA packaging motor contains a dodecameric connector at the vertex of the procapsid, with a central pore for DNA translocation. This portal connector serves as the foothold for pRNA binding to procapsid. Subsequent modeling of a connector/pRNA complex suggests that the pRNA of the phi29 DNA packaging motor exists as a hexameric complex serving as a sheath over the connector. The model of hexameric pRNA on the connector agrees with AFM images of the phi29 pRNA hexamer acquired in air and matches all distance parameters obtained from cross-linking, complementary modification, and chemical modification interference.

Ab initio molecular dynamics of Na⁺ and Mg²⁺ countercations at the backbone of RNA in water solution

The interactions between sodium or magnesium ions and phosphate groups of the RNA backbone represented as dinucleotide fragments in water solution have been studied using ab initio Born-Oppenheimer molecular dynamics. All systems have been simulated at 300 and 320 K. Sodium ions have mobility higher than that of the magnesium ions and readily change their position with respect to the phosphate groups, from directly bonded to completely solvated state, with a rough estimate of the lifetime of bonded Na(+) of about 20-30 ps. The coordination number of the sodium ions frequently changes in irregular intervals ranging from several femtoseconds to about 10 ps with the most frequently encountered coordination number five, followed by six. The magnesium ion is stable both as directly bonded to an oxygen atom from the phosphate group and completely solvated by water. In both states the Mg(2+) ion has exactly six oxygen atoms in the first coordination shell; moreover, during the whole simulation of more than 100 ps no exchange of ligand in the first coordination shells has been observed. Solvation of the terminal phosphate oxygen atoms by water molecules forming hydrogen bonds in different locations of the ions is also discussed. The stability of the system containing sodium ions essentially does not depend on the position of the ions with respect to the phosphate groups.