Thermal diffusion of nucleotides

Continuous iontronic chemotherapy reduces brain tumor growth in embryonic avian in vivo models

Local and long-lasting administration of potent chemotherapeutics is a promising therapeutic intervention to increase the efficiency of chemotherapy of hard-to-treat tumors such as the most lethal brain tumors, glioblastomas (GBM). However, despite high toxicity for GBM cells, potent chemotherapeutics such as gemcitabine (Gem) cannot be widely implemented as they do not efficiently cross the blood brain barrier (BBB). As an alternative method for continuous administration of Gem, we here operate freestanding iontronic pumps - "GemIPs" - equipped with a custom-synthesized ion exchange membrane (IEM) to treat a GBM tumor in an avian embryonic in vivo system. We compare GemIP treatment effects with a topical metronomic treatment and observe that a remarkable growth inhibition was only achieved with steady dosing via GemIPs. Daily topical drug administration (at the maximum dosage that was not lethal for the embryonic host organism) did not decrease tumor sizes, while both treatment regimes caused S-phase cell cycle arrest and apoptosis. We hypothesize that the pharmacodynamic effects generate different intratumoral drug concentration profiles for each technique, which causes this difference in outcome. We created a digital model of the experiment, which proposes a fast decay in the local drug concentration for the topical daily treatment, but a long-lasting high local concentration of Gem close to the tumor area with GemIPs. Continuous chemotherapy with iontronic devices opens new possibilities in cancer treatment: the long-lasting and highly local dosing of clinically available, potent chemotherapeutics to greatly enhance treatment efficiency without systemic side-effects. SIGNIFICANCE STATEMENT: Iontronic pumps (GemIPs) provide continuous and localized administration of the chemotherapeutic gemcitabine (Gem) for treating glioblastoma in vivo. By generating high and constant drug concentrations near the vascularized growing tumor, GemIPs offer an efficient and less harmful alternative to systemic administration. Continuous GemIP dosing resulted in remarkable growth inhibition, superior to daily topical Gem application at higher doses. Our digital modelling shows the advantages of iontronic chemotherapy in overcoming limitations of burst release and transient concentration profiles, and providing precise control over dosing profiles and local distribution. This technology holds promise for future implants, could revolutionize treatment strategies, and offers a new platform for studying the influence of timing and dosing dependencies of already-established drugs in the fight against hard-to-treat tumors.

Heat flows enrich prebiotic building blocks and enhance their reactivity

The emergence of biopolymer building blocks is a crucial step during the origins of life1-6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.

Colloid thermophoresis in the dilute electrolyte concentration regime: from theory to experiment

Colloid thermophoresis in aqueous media is vital for numerous applications in nanoscience and life sciences. To date, a general description of colloid thermophoresis in DI water has not been determined. Here, we describe a theoretical model within the framework of the Fokker-Planck formalism and the flickering cluster concept to describe the hydration entropy effect on the thermophoretic behaviour of colloids suspended in DI water and compare this to new experimental results. We built an experimental platform to allow for rapid and robust temperature control and investigate the thermophoretic behaviour of silica microspheres with different sizes at various background temperatures for comparison. In this work, the ionic shielding effect is accounted for by using the well-known Duhr-Dhont's model, and the hydration layer effect is determined using the developed theoretical model. For the latter, our model reveals that the sign of the Soret coefficient is governed by the interplay between the binding energy and the chemical potential of water molecules, which were found to be in the same order of magnitude. We show that our analysis accurately describes the experimental behaviour of colloidal particles that opens a new avenue for developing versatile trapping and separation techniques for various colloidal particles in aqueous systems according to their size and background temperature.

A heated rock crack captures and polymerizes primordial DNA and RNA

Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of complex monomer building blocks are required. Therefore, the dilution by diffusion poses a major problem before early life could establish a non-equilibrium of compartmentalization. Here, we explored a natural non-equilibrium habitat to polymerize RNA and DNA. A heat flux across thin rock cracks is shown to accumulate and maintain nucleotides. This boosts the polymerization to RNA and DNA inside the crack. Moreover, the polymers remain localized, aiding both the creation of longer polymers and fostering downstream evolutionary steps. In a closed system, we found single nucleotides concentrate 10⁴-fold at the bottom of the crack compared to the top after 24 hours. We detected enhanced polymerization for 2 different activation chemistries: aminoimidazole-activated DNA nucleotides and 2',3'-cyclic RNA nucleotides. The copolymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. Finite element models unravelled the combined polymerization and accumulation kinetics and indicated that the escape of the nucleotides from such a crack is negligible over a time span of years. The thermal non-equilibrium habitat establishes a cell-like compartment that actively accumulates nucleotides for polymerization and traps the resulting oligomers. We argue that the setting creates a pre-cellular non-equilibrium steady state for the first steps of molecular evolution.

Overlapping hydration shells in salt solutions causing non-monotonic Soret coefficients with varying concentration

We develop an intuitive picture that overlapping hydration shells in salt solutions cause non-monotonic Soret coefficients with varying concentration.

Targeted Chemotherapy of Glioblastoma Spheroids with an Iontronic Pump

Successful treatment of glioblastoma multiforme (GBM), the most lethal tumor of the brain, is presently hampered by (i) the limits of safe surgical resection and (ii) "shielding" of residual tumor cells from promising chemotherapeutic drugs such as Gemcitabine (Gem) by the blood brain barrier (BBB). Here, the vastly greater GBM cell-killing potency of Gem compared to the gold standard temozolomide is confirmed, moreover, it shows neuronal cells to be at least 104-fold less sensitive to Gem than GBM cells. The study also demonstrates the potential of an electronically-driven organic ion pump ("GemIP") to achieve controlled, targeted Gem delivery to GBM cells. Thus, GemIP-mediated Gem delivery is confirmed to be temporally and electrically controllable with pmol min-1 precision and electric addressing is linked to the efficient killing of GBM cell monolayers. Most strikingly, GemIP-mediated GEM delivery leads to the overt disintegration of targeted GBM tumor spheroids. Electrically-driven chemotherapy, here exemplified, has the potential to radically improve the efficacy of GBM adjuvant chemotherapy by enabling exquisitely-targeted and controllable delivery of drugs irrespective of whether these can cross the BBB.

Thermophoresis of biological and biocompatible compounds in aqueous solution

With rising popularity of microscale thermophoresis for the characterisation of protein-ligand binding reactions and possible applications in microfluidic devices, there is a growing interest in considering thermodiffusion in the context of life sciences. But although the understanding of thermodiffusion in non-polar mixtures has grown rapidly in recent years, predictions for associated mixtures like aqueous solutions remain challenging. This review aims to give an overview of the literature on thermodiffusion in aqueous systems, show the difficulties in theoretical description that arise from the non-ideal behaviour of water-mixtures, and highlight the relevance of thermodiffusion in a biological context. We find that the thermodiffusion in aqueous systems is dominated by contributions from heat of transfer, hydrogen bond interactions and charge effects. However, the separation of these effects is often difficult, especially in case of biological systems where a systematic exclusion of contributions may not be feasible.

Thermophoresis of a Colloidal Rod: Contributions of Charge and Grafted Polymers

In this study, we investigated the thermodiffusion behavior of a colloidal model system as a function of the Debye length, λ_DH, which is controlled by the ionic strength. Our system consists of an fd-virus grafted with poly(ethylene glycol) (PEG) with a molecular mass of 5000 g mol^-1. The results are compared with recent measurements on a bare fd-virus and with results of PEG. The diffusion coefficients of both viruses are comparable and increase with the increasing Debye length. The thermal diffusion coefficient, D_T, of the bare virus increases strongly with the Debye length, whereas D_T of the grafted fd-virus shows only a very weak increase. The Debye length dependence of both systems can be described with an expression derived for charged rods using the surface charge density and an offset of D_T as adjustable parameters. It turns out that the ratio of the determined surface charges is inverse to the ratio of the surfaces of the two systems, which means that the total charge remains almost constant. The determined offset of the grafted fd-virus describing the chemical contributions is the sum of D_T of PEG and the offset of the bare fd-virus. At high λ_DH, corresponding to the low ionic strength, the S_T values of both colloidal model systems approach each other. This implies a contribution from the polymer layer, which is strong at short λ_DH and fades out for the longer Debye lengths, when the electric double layer reaches further than the polymer chains and therefore dominates interactions with the surrounding water.

Quantification of tension to explain bias dependence of driven polymer translocation dynamics

Motivated by identifying the origin of the bias dependence of tension propagation, we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here, the motion of flexible polymer chains through a narrow pore is simulated using Langevin dynamics. We measure tension forces, bead velocities, bead distances, and bond angles along the polymer at all stages of translocation with unprecedented precision. Measurements are done at a standard temperature used in simulations and at zero temperature to pin down the effect of fluctuations. The measured quantities were found to give qualitatively similar characteristics, but the bias dependence could be determined only using tension force. We find that in the scaling relation τ∼N^{β}f_{d}^{α} for translocation time τ, the polymer length N, and the bias force f_{d}, the increase of the exponent β with bias is caused by center-of-mass diffusion of the polymer toward the pore on the cis side. We find that this diffusion also causes the exponent α to deviate from the ideal value -1. The bias dependence of β was found to result from combination of diffusion and pore friction and so be relevant for polymers that are too short to be considered asymptotically long. The effect is relevant in experiments all of which are made using polymers whose lengths are far below the asymptotic limit. Thereby, our results also corroborate the theoretical prediction by Sakaue's theory [Polymers 8, 424 (2016)2073-436010.3390/polym8120424] that there should not be bias dependence of β for asymptotically long polymers. By excluding fluctuations we also show that monomer crowding at the pore exit cannot have a measurable effect on translocation dynamics under realistic conditions.

Proton gradients and pH oscillations emerge from heat flow at the microscale

Proton gradients are essential for biological systems. They not only drive the synthesis of ATP, but initiate molecule degradation and recycling inside lysosomes. However, the high mobility and permeability of protons through membranes make pH gradients very hard to sustain in vitro. Here we report that heat flow across a water-filled chamber forms and sustains stable pH gradients. Charged molecules accumulate by convection and thermophoresis better than uncharged species. In a dissociation reaction, this imbalances the reaction equilibrium and creates a difference in pH. In solutions of amino acids, phosphate, or nucleotides, we achieve pH differences of up to 2 pH units. The same mechanism cycles biomolecules by convection in the created proton gradient. This implements a feedback between biomolecules and a cyclic variation of the pH. The finding provides a mechanism to create a self-sustained proton gradient to drive biochemical reactions.

Role of Hydrogen Bonding of Cyclodextrin-Drug Complexes Probed by Thermodiffusion

Temperature gradient-induced migration of biomolecules, known as thermophoresis or thermodiffusion, changes upon ligand binding. In recent years, this effect has been used to determine protein-ligand binding constants. The mechanism through which thermodiffusive properties change when complexes are formed, however, is not understood. An important contribution to thermodiffusive properties originates from the thermal response of hydrogen bonds. Because there is a considerable difference between the degree of solvation of the protein-ligand complex and its isolated components, ligand-binding is accompanied by a significant change in hydration. The aim of the present work is therefore to investigate the role played by hydrogen bonding on the change in thermodiffusive behavior upon ligand-binding. As a model system, we use cyclodextrins (CDs) and acetylsalicylic acid (ASA), where quite a significant change in hydration is expected and where no conformational changes occur when a CD/ASA complex is formed in aqueous solution. Thermophoresis was investigated in the temperature range of 10-50 °C by infrared thermal diffusion forced Rayleigh scattering. Nuclear magnetic resonance measurements were performed at 25 °C to obtain information about the structure of the complexes. All CD/ASA complexes show a stronger affinity toward regions of lower temperature compared to the free CDs. We found that the temperature sensitivity of thermophoresis correlates with the 1-octanol/water partition coefficient. This observation not only establishes the relation between thermodiffusion and degree of hydrogen bonding but also opens the possibility to relate thermodiffusive properties of complexes to their partition coefficient, which cannot be determined otherwise. This concept is especially interesting for protein-ligand complexes where the protein undergoes a conformational change, different from the CD/ASA complexes, giving rise to additional changes in their hydrophilicity.

Thermophoresis of cyclic oligosaccharides in polar solvents

Cyclodextrins are cyclic oligosaccharides which are interesting as drug delivery systems, because they can be used as containers for pharmaceutical substances. We studied the Ludwig-Soret effect of [Formula: see text]-, [Formula: see text]-, [Formula: see text]- and methyl-[Formula: see text]-cyclodextrin in water and formamide by infrared thermal diffusion forced Rayleigh scattering (IR-TDFRS). In water the Soret coefficient, S _T, of [Formula: see text]-, [Formula: see text]- and [Formula: see text]-cyclodextrin increases with increasing temperature and shows a sign change from negative to positive around T = 35 ^° C, while S _T of methyl-[Formula: see text]-cyclodextrin is positive in the entire investigated temperature. In formamide S _T-values of all cyclodextrins coincide and show a slight decrease with temperature. We discuss the obtained results and relate the S _T-values to the different hydrogen bonding capabilities of the cyclodextrins and the used solvents. It turns out that the change of S _T with temperature correlates with the partition coefficient, logP, which indicates that more hydrophilic substances show a more pronounced temperature sensitivity of S _T. Additionally we obtained a surprising result measuring the refractive index contrast factor with temperature, [Formula: see text] of cyclodextrins in formamide, which might be explained by a complex formation between cyclodextrins and formamide.

Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth.

Improved lateral heat spreading performance for polyvinylidene fluoride composite film comprising silver nanowire in light-emitting diode

Silver nanowire (AgNW) attracts great attention as a heat dissipation material due to its excellent thermal transfer property which exceeds most traditional heat sink materials.

Mechanism of short-pulse-induced solute migration in comparison to continuous-light-driven thermal diffusion

Short-pulse-induced and continuous-light-driven solute migrations are distinguished based on the composite time rate of photo absorption and intra-molecular excess energy redistribution relative to that of inter-molecular excess energy transfer.

Ludwig-Soret effect of aqueous solutions of ethylene glycol oligomers, crown ethers, and glycerol: Temperature, molecular weight, and hydrogen bond effect

The thermal diffusion, also called the Ludwig-Soret effect, of aqueous solutions of ethylene glycol oligomers, crown ethers, and glycerol is investigated as a function of temperature by thermal diffusion forced Rayleigh scattering. The Soret coefficient, ST, and the thermal diffusion coefficient, DT, show a linear temperature dependence for all studied compounds in the investigated temperature range. The magnitudes and the slopes of ST and DT vary with the chemical structure of the solute molecules. All studied molecules contain ether and/or hydroxyl groups, which can act as acceptor or donor to form hydrogen bonds, respectively. By introducing the number of donor and acceptor sites of each solute molecule, we can express their hydrogen bond capability. ST and DT can be described by an empirical equation depending on the difference of donor minus acceptor sites and the molecular weight of the solute molecule.

Molar mass and temperature dependence of the thermodiffusion of polyethylene oxide in water/ethanol mixtures

In this work, we study the molar mass dependence of the thermodiffusion of polyethylene oxide at different temperatures in ethanol, water/ethanol mixture (c(water) = 0.7), and water in a molar mass range up to M(w) = 180,000 g/mol. Due to the low solubility of polyethylene oxide oligomers in ethanol the measurements are limited up to M(w) = 2200 g/mol. The specific water/ethanol concentration 0.7 has been chosen, because at this weight fraction the thermal diffusion coefficient, D(T), of water/ethanol vanishes so that the system can be treated as a pseudo binary mixture. The addition of ethanol will degrade the solvent quality, so that we expect a change of the interaction energies between polymer and solvent. The analysis of the experimental data within a theoretical model shows the need of a refined model, which takes specific interactions into account.

Thermodiffusion, molecular diffusion and Soret coefficient of binary and ternary mixtures of n-hexane, n-dodecane and toluene

In this study, the thermodiffusion, molecular diffusion, and Soret coefficients of 12 binary mixtures composed of toluene, n-hexane and n-dodecane in the whole range of concentrations at atmospheric pressure and temperatures of 298.15 K and 308.15 K have been determined. The experimental measurements have been carried out using the Thermogravitational Column, the Sliding Symmetric Tubes and the Thermal Diffusion Forced Rayleigh Scattering techniques. The results obtained using the different techniques show a maximum deviation of 9% for the thermodiffusion coefficient, 8% for the molecular diffusion coefficient and 2% for the Soret coefficient. For the first time we report a decrease of the thermodiffusion coefficient with increasing ratio of the thermal expansion coefficient and viscosity for a binary mixture of an organic ring compound with a short n-alkane. This observation is discussed in terms of interactions between the different components. Additionally, the thermogravitational technique has been used to measure the thermodiffusion coefficients of four ternary mixtures consisting of toluene, n-hexane and n-dodecane at 298.15 K. In order to complete the study, the values obtained for the molecular diffusion coefficient in binary mixtures, and the thermodiffusion coefficient of binary and ternary mixtures have been compared with recently derived correlations.

How does thermodiffusion of aqueous solutions depend on concentration and hydrophobicity?

The thermal diffusion of aqueous solutions of mono-, di-ethylene glycols, poly(ethylene glycol), methanol, and glycerol is investigated systematically as a function of concentration using the Thermal Diffusion Forced Rayleigh Scattering (TDFRS). For all investigated binary mixtures, the Soret coefficient, S(T), decays with increasing concentration of the non-aqueous component showing two regions. For aqueous solution of ethylene glycol, at a very low solute content the decay is steep, while it becomes less steep for higher solute concentration. All mixtures show a sign change of S(T) with concentration. The sign change concentration is discussed with respect to chemical structures of solute molecules and the partition coefficient, log p. It turns out that the number of hydroxyl groups plays an important role. For the investigated aqueous mixtures, we find empirical linear relations between the sign change concentration and the ratio of the number of hydroxyl groups to the number of carbon atoms as well as the partition coefficient, log p.

Isothermal behavior of the Soret effect in nonionic microemulsions: size variation by using different n-alkanes

In this work we investigate the thermodiffusion behavior of microemulsion droplets of the type H2O/n-alkane/C12E5 (pentaethylene glycol monododecyl ether) using the n-alkanes: n-octane, n-decane, n-dodecane, and n-tetradecane. In order to determine the thermodiffusion behavior of these microemulsion droplets, we apply the infrared thermal diffusion forced Rayleigh scattering (IR-TDFRS) technique. We measure the Soret coefficient (ST) as function of the structure upon approaching the emulsification failure boundary (efb) and as a function of the radius of the spherical o/w microemulsion droplets close to the efb. By varying the chain length of the n-alkanes, we are able to study the thermodiffusion behavior of spherical o/w microemulsion droplets of different sizes at the same temperature. In the investigated range a linear dependence of the Soret coefficient as function of the radius was found. By use of a proposed relationship between the Soret coefficient and the temperature dependence of the interfacial tension, the transition layer l could be determined for the first time. Additionally, small angle neutron scattering (SANS) experiments are performed to determine the size and to prove that the shape of the microemulsion droplets is spherical close to the efb. Accordingly, the scattering curves could be quantitatively described by a combination of a spherical core-shell form factor and sticky hard sphere structure factor.

Alkali halide solutions under thermal gradients: soret coefficients and heat transfer mechanisms

We report an extensive analysis of the non-equilibrium response of alkali halide aqueous solutions (Na(+)/K(+)-Cl(-)) to thermal gradients using state of the art non-equilibrium molecular dynamics simulations and thermal diffusion forced Rayleigh scattering experiments. The coupling between the thermal gradient and the resulting ionic salt mass flux is quantified through the Soret coefficient. We find the Soret coefficient is of the order of 10(-3) K(-1) for a wide range of concentrations. These relatively simple solutions feature a very rich behavior. The Soret coefficient decreases with concentration at high temperatures (higher than T ∼ 315 K), whereas it increases at lower temperatures. In agreement with previous experiments, we find evidence for sign inversion in the Soret coefficient of NaCl and KCl solutions. We use an atomistic non-equilibrium molecular dynamics approach to compute the Soret coefficients in a wide range of conditions and to attain further microscopic insight on the heat transport mechanism and the behavior of the Soret coefficient in aqueous solutions. The models employed in this work reproduce the magnitude of the Soret coefficient, and the general dependence of this coefficient with temperature and salt concentration. We use the computer simulations as a microscopic approach to establish a correlation between the sign and magnitude of the Soret coefficients and ionic solvation and hydrogen bond structure of the solutions. Finally, we report an analysis of heat transport in ionic solution by quantifying the solution thermal conductivity as a function of concentration. The simulations accurately reproduce the decrease of the thermal conductivity with increasing salt concentration that is observed in experiments. An explanation of this behavior is provided.

Escalation of polymerization in a thermal gradient

For the emergence of early life, the formation of biopolymers such as RNA is essential. However, the addition of nucleotide monomers to existing oligonucleotides requires millimolar concentrations. Even in such optimistic settings, no polymerization of RNA longer than about 20 bases could be demonstrated. How then could self-replicating ribozymes appear, for which recent experiments suggest a minimal length of 200 nt? Here, we demonstrate a mechanism to bridge this gap: the escalated polymerization of nucleotides by a spatially confined thermal gradient. The gradient accumulates monomers by thermophoresis and convection while retaining longer polymers exponentially better. Polymerization and accumulation become mutually self-enhancing and result in a hyperexponential escalation of polymer length. We describe this escalation theoretically under the conservative assumption of reversible polymerization. Taking into account the separately measured thermophoretic properties of RNA, we extrapolate the results for primordial RNA polymerization inside a temperature gradient in pores or fissures of rocks. With a dilute, nanomolar concentration of monomers the model predicts that a pore length of 5 cm and a temperature difference of 10 K suffice to polymerize 200-mers of RNA in micromolar concentrations. The probability to generate these long RNAs is raised by a factor of >10(600) compared with polymerization in a physical equilibrium. We experimentally validate the theory with the reversible polymerization of DNA blocks in a laser-driven thermal trap. The results confirm that a thermal gradient can significantly enlarge the available sequence space for the emergence of catalytically active polymers.