Ligand-dependent exponential amplification of a self-replicating L-RNA enzyme

A nuclease-resistant RNA enzyme, constructed entirely from L-ribonucleotides, was shown to undergo ligand-dependent, self-sustained replication with exponential growth. The catalytic motif is based on a previously described RNA ligase that can undergo either self- or cross-replication but had been limited in its application to ligand sensing due to its susceptibility to degradation by ribonucleases. The self-replicating RNA enzyme and its RNA substrates were prepared synthetically from either D- or L-nucleoside phosphoramidites. The D and L reaction systems undergo isothermal, ligand-dependent exponential amplification in the same manner, but only the l system is impervious to ribonucleases and can operate, for example, in the presence of human serum. This system has potential for the quantitative detection of various ligands that are present within biological or environmental samples. In addition, this work provides the first demonstration of the self-sustained exponential amplification of nonbiological molecules.     

Approaching the direct exponential curve resolution algorithm from a maximum likelihood perspective

The implementation of maximum likelihood parallel factor analysis (MLPARAFAC) in conjunction with the direct exponential curve resolution algorithm (DECRA) is described. DECRA takes advantage of the intrinsic exponential structure of some bilinear data sets to produce trilinear data by a simple shifting scheme, but this manipulation generates an error structure that is not optimally handled by traditional three-way chemometrics methods such as TLD and PARAFAC. In this work, the effects of these violations are studied using simulated and experimental data used in conjunction with the well-established TLD and PARAFAC. The results obtained by both methods are compared with the results obtained by MLPARAFAC, which is a method designed to optimally accomodate a variety of measurement error structures. The impact on the estimates of different parameters linked to the data sets and the DECRA method is investigated using simulated data. The results indicate that PARAFAC produces estimates of much poorer quality than TLD and MLPARAFAC. Also, it was found that the quality TLD estimates was comparable or only marginally poorer than the MLPARAFAC estimates. A number of commonly used algorithms were also compared to MLPARAFAC using two sets of published experimental data from kinetic studies. The MLPARAFAC estimates of rate constants were more precise than the other methods examined.     

Transfer of stereochemical information in a minimal self-replicating system

[structure: see text]. The rational design, synthesis, and characterization of a minimal self-replicating system based on a 1,3-dipolar cycloaddition between a nitrone and a maleimide is presented. The importance of molecular recognition in this system is demonstrated using a competitive inhibitor. Doping experiments demonstrate that only one of the two diastereoisomeric products of the cycloaddition reaction is capable of acting as an efficient template for its own formation, accelerating the reaction between the nitrone and maleimide and controlling the stereochemical outcome of the reaction.     

Bifurcation diagrams and Turing patterns in a chemical self-replicating reaction-diffusion system with cross diffusion

Chemical self-replication of oligonucleotides and helical peptides exhibits the so-called square root rate law. Based on this rate we extend our previous work on ideal replicators to include the square root rate and other possible nonlinearities, which we couple with an enzymatic sink. For this generalized model, we consider the role of cross diffusion in pattern formation, and we obtain exact general relations for the Poincare-Adronov-Hopf and Turing bifurcations, and our generalized results include the Higgins, Autocatalator, and Templator models as specific cases.     

From exponential to linear growth in polyelectrolyte multilayers

There exist two types of polyelectrolyte multilayers: those whose thickness increases linearly with the number of deposition steps, which are nicely structured, and those whose thickness increases exponentially, which resembles hydrogels. This simple picture has recently slightly evolved with the finding that some exponentially growing films enter into a linear growth phase after a certain number of deposition steps. In this study, we investigate the buildup process of hyaluronic acid/poly(L-lysine) (HA/PLL) multilayers that constitute one of the best known exponentially growing systems. The films are built by using two deposition methods: the well-known dipping method and the more recent spraying method where the polyelectrolyte solutions are sprayed alternately onto a vertical substrate. The goal of this study is twofold. First, we investigate the influence of the main parameters (i.e., spraying rate and spraying time) of the spraying method on the film growth process. We find that, as for the dipping method, the film thickness first evolves exponentially with the number of deposition steps, and after a given number of deposition steps, it follows a linear evolution. We find that similar behavior is observed with the dipping method. Second, because the spraying method allows the very fine variation of the different parameters of the buildup, we use this method to investigate the exponential-to-linear transition. We find that this transition always takes place after about 12 deposition steps whatever the values of the parameters controlling the deposition process. We discuss our results in light of a model proposed by Hübsch et al. (Hübsch, E.; Ball, V.; Senger, B.; Decher, G.; Voegel, J. C.; Schaaf, P. Langmuir 2004, 20, 1980-1985) and later by Salom?ki et al. (Salom?ki, M.; Vinokurov, I. A.; Kankare, J. Langmuir 2005, 21, 11232-11240) in which it is assumed that the exponential-to-linear transition is due to a film restructuring that progressively forbids the diffusion of one of the polyelectrolytes constituting the film over part of the film. This "forbidden" zone then grows with the number of deposition steps so that the outer zone of the film that is still concerned with diffusion keeps a constant thickness and moves upward as the total film thickness increases.     

Approaching a persistent favorskii zwitterion

2-Phenalanone has been synthesized via a double Curtius procedure and converted to the conjugate acid of 2-phenalenylium oxide, a potential persistent Favorskii zwitterion.     

Relaxation times in a system with exponential transition probabilities

Thermal vibrational relaxation times (τ) are calculated for two properly normalzed exponential transition probability models. If both threshold for reaction (E₀ and a constant related to average energy lost in a collision (γ) are assumed to be temperature independent, τ increases sharply with temperature. A simple analytic formula is derived for τ, valid for γ/kT < 1 and for E₀/kT ? 15.     

Elucidating the origin of diastereoselectivity in a self-replicating system: selfishness versus altruism

We have investigated a diastereoselective self‐replicating system based on a cycloaddition of a fulvene derivative and a maleimide using a two‐pronged approach of combining NMR spectroscopy with computational modelling. Two diastereomers are formed with identical rates in the absence of replication. When replication is enabled, one diastereomer takes over the resources as a “selfish” autocatalyst, while exploiting the competitor as a weak “altruist”, resulting in a diastereoselectivity of 16:1. We applied 1D and 2D NMR spectroscopic techniques supported by ab initio chemical shifts as well as ab initio molecular dynamics simulations to study the structure and dynamics of the underlying network. This powerful combination allowed us to decipher the energetic and structural rationale behind the observed behaviour, while static computational methods currently used in the field did not.     

Approaching chemical accuracy with quantum Monte Carlo

A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space.     

Phased fiber growth in a peptide conjugate: aggregation and disaggregation studies

A glycine-rich, short pentapeptide conjugate 6, derived from the highly conserved copper-binding octarepeat region of the prion protein, exhibits a tendency to self-aggregate in a time-dependent fashion. Aging of 6 afforded an insight into the phased growth of spherical prefibrillar structures to fibers of long persistence length, as observed by a combination of microscopic techniques. Interestingly, growth of these fibers was inhibited by colchicine, a known inhibitor of microtubule polymerization in a concentration dependent fashion. This study offers an intriguing insight into the occurrence of prefibrillar intermediates on the path to the formation of full length peptide fibers. It is also envisaged that constructs such as 6 may also serve as simple models to study chemical intervention of protein aggregation.     

Multicompartment films made of alternate polyelectrolyte multilayers of exponential and linear growth

The layer by layer deposition process of polyelectrolytes is used to construct films equipped with several compartments containing "free polyelectrolytes". Each compartment corresponds to a stratum of an exponentially growing polyelectrolyte multilayer film, and two consecutive compartments are separated by a stratum composed of a linearly growing multilayer that acts as a barrier preventing polyelectrolyte diffusion from one compartment to another. We use hyaluronic acid/poly(L-lysine) as the system to build the compartments and the poly(styrene sulfonate)/poly(allylamine) system for the barrier. Using confocal microscopy, it is shown that poly(L-lysine) diffuses only within the compartment in which it was initially introduced during the film construction and is thus unable to cross the barriers. Using fluorescein isothiocyanate as a pH indicator, it is also shown that although poly(styrene sulfonate)/poly(allylamine) multilayers act as a barrier for polyelectrolytes, they do not prevent proton diffusion through the film. Such films open the route for multiple functionalization of biomaterial coatings.     

Equilibrium theory of a “soft sphere” fluid with exponential interaction

Odessa Technological Institute for Industrial Refrigeration. Translated from Zhurnal Strukturnoi Khimii, Vol. 29, No. 5, pp. 84–88, September–October, 1988.     

Approaching the self-consistency challenge of electrocatalysis with theory and computation

This opinion piece centers around challenges involved in developing first-principles electrochemical methods. In recent years, theory and computation have become indispensable tools to navigate the parameter space that controls the activity and stability of electrocatalytic materials and electrochemical devices. Viable methods process as input details on materials structure, composition and reaction conditions. Their output includes metrics for stability and activity, phase diagrams, as well as mechanistic insights on reaction mechanisms and pathways. The core challenge, connecting input to output, is a self-consistency problem that couples the electrode potential to variables for the electronic structure of the solid electrode, solvent properties and ion distributions in the electrolyte as well as specific properties of a boundary region in-between. We will discuss a theoretical framework and computational approaches that strive to accomplish this feat.     

Room-temperature Wurtzite ZnS nanocrystal growth on Zn finger-like peptide nanotubes by controlling their unfolding peptide structures

ZnS nanocrystal, a class of wide-gap semiconductors, has shown interesting optical, electrical, and optoelectric properties via quantum confinement. For those applications, phase controls of ZnS nanocrystals and nanowires were critical to tune their physical properties to the appropriate ones. The wurtzite ZnS nanocrystal growth at room temperature is the useful fabrication; however, the most stable ZnS structure in nanoscale is the zinc blende (cubic) structure, and scientists have just begun exploring the room-temperature synthesis of the wurtzite (hexagonal) structure of ZnS nanocrystals. In this report, we applied the Zn finger-like peptides as templates to control the phase of ZnS nanocrystals to the wurtzite structure at room temperature. The peptide nanotubes, consisting of a 20 amino acids (VAL-CYS-ALA-THR-CYS-GLU-GLN-ILE-ALA-ASP-SER-GLN-HIS-ARG-SER-HIS-ARG-GLN-MET-VAL, M1 peptide) synthesized based on the peptide motif of the Influenza Virus Matrix Protein M1, could grow the wurtzite ZnS nanocrystals on the nanotube templates in solution. In the M1 protein, the unfolding process of the helical peptide motif via pH change creates a linker region between N- and C-terminated helical domains that contains a Zn finger-like Cys2His2 motif. Because the higher pH increases the uptake of Zn ions in the Cys2His2 motif of the M1 peptide by unfolding more helical domains, the pH change can essentially control the size and the number of the nucleation sites in the M1 peptides to grow ZnS nanocrystals with desired phases. Here we optimized the nucleation sites in the M1 peptides by unfolding them via pH change to obtain highly monodisperse and crystalline wurtzite ZnS nanocrystals on the template nanotubes at room temperature. This type of peptide-induced biomineralization technique will provide a clean and reproducible method to produce semiconductor nanotubes due to its efficient nanocrystal formation, and the band gaps of resulting nanotubes can also be tuned simply by phase control of ZnS nanocrystal coatings via the optimization of the unfolding peptide structures.     

Control of antigen presentation with a photoreleasable agonist peptide

The immunological synapse is a specialized intercellular junction between a T cell and a target cell that orchestrates the engagement of receptors and ligands in space and time as a means of regulating function. Here we introduce a reagent for controlling the spatial and temporal presentation of natural antigen to T cells. Moth cytochrome c (88-103) peptide (MCC), an agonist to the murine T cell receptor AND when presented in the context of H2 IEk major histocompatibility complex (IEk), was synthesized with the side-chain amine of Lys99 conjugated to a photosensitive protecting group, 6-nitroveratryloxycarbonyl (NVOC). Cells plated on supported bilayers displaying mobile intercellular adhesion molecule-1 (ICAM-1) and NVOC-MCC loaded IEk did not form immunological synapses and exhibited low intracellular calcium levels, similar to cells presented with self-peptide. Irradiation with UV light was sufficient to restore agonist activity in situ.     

Reversible photocontrol of peptide conformation with a rhodopsin-like photoswitch

Reversible photocontrol of biomolecules requires chromophores that can efficiently undergo large conformational changes upon exposure to wavelengths of light that are compatible with living systems. We designed a benzylidene-pyrroline chromophore that mimics the Schiff base of rhodopsin and can be used to introduce light-switchable intramolecular cross-links in peptides and proteins. This new class of photoswitch undergoes an ~10 ? change in end-to-end distance upon isomerization and can be used to control the conformation of a target peptide efficiently and reversibly using, alternately, violet (400 nm) and blue (446 nm) light.