Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies

Most functional nanosystems in living organisms are constructed using multimeric assemblies that provide multiple advantages over their monomeric counterparts such as cooperative or anti-cooperative responses, integration of multiple signals and self-regulation. Inspired by these natural nanosystems, chemists have been synthesizing self-assembled supramolecular systems over the last 50 years with increasing complexity with applications ranging from biosensing, drug delivery, synthetic biology, and system chemistry. Although many advances have been made concerning the design principles of novel molecular architectures and chemistries, little is still known, however, about how to program their dynamic of assembly so that they can assemble at the required concentration and with the right sensitivity. Here, we used synthetic DNA assemblies and double-mutant cycle analysis to explore the thermodynamic basis to program the cooperativity of molecular assemblies. The results presented here exemplify how programmable molecular assemblies can be efficiently built by fusing interacting domains and optimizing their compaction. They may also provide the rational basis for understanding the thermodynamic and mechanistic principles driving the evolution of multimeric biological complexes.

Programing Chemical Communication: Allostery vs Multivalent Mechanism

The emergence of life has relied on chemical communication and the ability to integrate multiple chemical inputs into a specific output. Two mechanisms are typically employed by nature to do so: allostery and multivalent activation. Although a better understanding of allostery has recently provided a variety of strategies to optimize the binding affinity, sensitivity, and specificity of molecular switches, mechanisms relying on multivalent activation remain poorly understood. As a proof of concept to compare the thermodynamic basis and design principles of both mechanisms, we have engineered a highly programmable DNA-based switch that can be triggered by either a multivalent or an allosteric DNA activator. By precisely designing the binding interface of the multivalent activator, we show that the affinity, dynamic range, and activated half-life of the molecular switch can be programed with even more versatility than when using an allosteric activator. The simplicity by which the activation properties of molecular switches can be rationally tuned using multivalent assembly suggests that it may find many applications in biosensing, drug delivery, synthetic biology, and molecular computation fields, where precise control over the transduction of binding events into a specific output is key.

Functional advantages of building nanosystems using multiple molecular components

Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.

Programmable self-regulated molecular buffers for precise sustained drug delivery

Unlike artificial nanosystems, biological systems are ideally engineered to respond to their environment. As such, natural molecular buffers ensure precise and quantitative delivery of specific molecules through self-regulated mechanisms based on Le Chatelier's principle. Here, we apply this principle to design self-regulated nucleic acid molecular buffers for the chemotherapeutic drug doxorubicin and the antimalarial agent quinine. We show that these aptamer-based buffers can be programmed to maintain any specific desired concentration of free drug both in vitro and in vivo and enable the optimization of the chemical stability, partition coefficient, pharmacokinetics and biodistribution of the drug. These programmable buffers can be built from any polymer and should improve patient therapeutic outcome by enhancing drug activity and minimizing adverse effects and dosage frequency.

Triazine-based molecular glasses frustrate the crystallization of barbiturates

Hydrogen bonding is a key element in crystal engineering to direct crystal packing. Here, hydrogen bonding with molecular glasses is rather exploited to thwart crystallization.

Programmable DNA switches and their applications

DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.

Pathogens in children with severe combined immune deficiency disease or AIDS

We evaluated the frequency and severity of illnesses caused by various microbial pathogens in 15 children with severe combined immune deficiency disease (SCID) and 8 with acquired immune deficiency syndrome (AIDS). There were 35 viral, 23 bacterial, 19 mycotic and 13 parasitic infections. Nineteen of the 23 patients died of infection; Pneumocystis carinii pneumonia, giant-cell pneumonia due to paramyxoviruses and various disseminated viral infections were responsible for most deaths in both groups. The emerging role of paramyxoviruses was illustrated by the fact that they were responsible for giant-cell pneumonia in seven patients. Viral enteric infections were frequent in both groups. The variety of infectious microorganisms and the severity of resulting illnesses in the patients with AIDS were similar to those in the patients with SCID.

Bactericidal activity and killing rate of serum from volunteers receiving pefloxacin alone or in combination with amikacin

Serum bactericidal activities (SBAs) were studied after intravenous administration of pefloxacin (8 mg/kg) and amikacin (7.5 mg/kg) alone or in combination to 15 human volunteers. About 10 strains each of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus were tested. The serum levels of pefloxacin were measured microbiologically by using E. coli KP 1976-712 as the test organism at 0, 30, 60, 120, and 720 min after infusion; at 0, 30, 60, and 720 min these levels were 7 +/- 1.4, 5 +/- 0.8, 4.5 +/- 0.7, and 2.1 +/- 0.6 mg/liter (mean +/- standard deviation), respectively, with a terminal half-life of 10 h. The serum levels of pefloxacin in the presence of amikacin were measured similarly; 1% sodium polyanethol sulfonate was added to the agar to inactivate amikacin. Treatment with pefloxacin alone resulted in high SBAs against E. coli, K. pneumoniae strains susceptible to cephalothin, and Staphylococcus aureus at the peak concentration; 81 to 100% of the sera had SBAs of greater than or equal to 1:8. However, treatment with pefloxacin alone resulted in low SBAs against K. pneumoniae strains resistant to cephalothin and P. aeruginosa; only 34% of the sera had SBAs of greater than or equal to 1:8. At trough concentrations the percentages of sera with SBAs greater than or equal to 1:8 were 75 to 83% (E. coli), 9 to 27% (K. pneumoniae), 0% (P. aeruginosa), and 10% (S. aureus). The combination of pefloxacin plus amikacin was most often additive; the peak activity was due to amikacin, and the trough activity was due to pefloxacin. Occasionally antagonism occurred with P. aeruginosa, K. pneumoniae, and S. aureus strains. These observations were confirmed by the killing curves in pooled serum obtained at peak and trough levels. Regrowth was observed for seven strains of P. aeruginosa treated with pefloxacin alone; amikacin seemed to prevent this phenomenon.