Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements.
ABSTRACT: DNA nanotubes provide a programmable architecture for molecular self-assembly and can serve as model systems for one-dimensional biomolecular assemblies. While a variety of DNA nanotubes have been synthesized and employed as models for natural biopolymers, an extensive investigation of DNA nanotube kinetics and thermodynamics has been lacking. Using total internal reflection microscopy, DNA nanotube polymerization was monitored in real time at the single filament level over a wide range of free monomer concentrations and temperatures. The measured polymerization rates were subjected to a global nonlinear fit based on polymerization theory in order to simultaneously extract kinetic and thermodynamic parameters. For the DNA nanotubes used in this study, the association rate constant is (5.99 ± 0.15) × 105 M-1 s-1, the enthalpy is 87.9 ± 2.0 kcal mol-1, and the entropy is 0.252 ± 0.006 kcal mol-1 K-1. The qualitative and quantitative similarities between the kinetics of DNA nanotubes, actin filaments, and microtubules polymerization highlight the prospect of building complex dynamic systems from DNA molecules inspired by biological architecture.
Project description:Short single-stranded DNA (ssDNA) has emerged as the natural polymer of choice for noncovalently functionalizing photoluminescent single-walled carbon nanotubes. In addition, specific empirically identified DNA sequences can be used to separate single species (chiralities) of nanotubes, with an exceptionally high purity. Currently, only limited general principles exist for designing DNA-nanotube hybrids amenable to separation processes, due in part to an incomplete understanding of the fundamental interactions between a DNA sequence and a specific nanotube structure, whereas even less is known in the design of nanotube-based sensors with determined optical properties. We therefore developed a combined experimental and analysis platform on the basis of time-resolved near-infrared fluorescence spectroscopy to extract the complete set of photoluminescence parameters that characterizes DNA-nanotube hybrids. Here, we systematically investigated the affinity of the d(GT)n oligonucleotide family for structurally defined carbon nanotubes by measuring photoluminescence response of the nanotube upon oligonucleotide displacement. We found, surprisingly, that the rate of displacement of the oligonucleotides is independent of the coverage on the nanotube, as inferred through the intrinsic optical properties of the hybrid. The kinetics of intensity modulation is essentially a single-exponential, and the time constants, which quantify the stability of DNA binding, span an order of magnitude. Surprisingly, these time constants do not depend on the intrinsic optical parameters within the hybrids, suggesting that the DNA-nanotube stability is not due to increased nanotube surface coverage by DNA. Further, a principal component analysis of the excitation and emission shifts along with intensity enhancement at equilibrium accurately identified the (8,6) nanotube as the partner chirality to (GT)6 ssDNA. When combined, the chirality-resolved equilibrium and kinetics data can guide the development of the DNA-nanotube pairs, with tunable stability and optical modulation. Additionally, this high-throughput optical platform could function as a primary screen for mapping the DNA-chirality recognition phase space.
Project description:We present the results from extensive molecular dynamics simulations to study the effect of varying interaction strength, ?NT-OW, between the nanotube atoms and water's oxygen atom. We find the existence of a narrow transition region (?NT-OW ? 0.05 - 0.075 kcal/mol) in which water occupancy within a nanotube and flux through it increases dramatically with increasing ?NT-OW, with the exact location defined by nanotube diameter and length. This transition region narrows with increasing nanotube diameter to nearly a step-change in water transport from no flow to high water flux between ?NT-OW= 0.05 kcal/mol to 0.055 kcal/mol for tube diameter 1.6 nm. Interestingly, this transition region (?NT-OW= 0.05 - 0.075 kcal/mol) also coincides with water contact angles close to 90° on an unrolled nanotube surface hinting at a fundamental link between nanotube wetting characteristics and water transport through it. Finally, we find that the observed water flux is proportional to the average water occupancy divided by the average residence time within the nanotube, with a proportionality constant found to be 0.36, independent of the nanotube diameter and length.
Project description:Titanium dioxide (TiO₂) nanotube and its hybrid nanotubes (with various metal oxides such as Ta₂O₅, Nb₂O₅, ZrO2, and SiO₂) were fabricated by the sol-gel polymerization in the ethanol gels formed by simple l-lysine-based organogelator. The self-assembled nanofibers (gel fibers) formed by the gelator functioned as a template. The different calcination temperatures gave TiO₂ nanotubes with various crystalline structures; e.g., anatase TiO₂ nanotube was obtained by calcination at 600 °C, and rutile TiO₂ nanotube was fabricated at a calcination temperature of 750 °C. In the metal oxide/TiO₂ hybrid nanotubes, the metal oxide species were uniformly dispersed in the TiO₂ nanotube, and the percent content of metal oxide species was found to correspond closely to the feed ratio of the raw materials. This result indicated that the composition ratio of hybrid nanotubes was controllable by the feed ratio of the raw materials. It was found that the metal oxide species inhibited the crystalline phase transition of TiO₂ from anatase to rutile. Furthermore, the success of the hybridization of other metal oxides (except for TiO₂) indicated the usefulness of the organogel route as one of the fabrication methods of metal oxide nanotubes.
Project description:We study the conformational equilibrium between B-to-A forms of ds-DNA adsorbed onto a single-walled carbon nanotube (SWNT) using free energy profile calculations based on all-atom molecular dynamics simulations. The potential of mean force (PMF) of the B-to-A transition of ds-DNA in the presence of an uncharged (10,0) carbon nanotube for two dodecamers with poly-AT or poly-GC sequences is calculated as a function of a root-mean-square-distance (ΔRMSD) difference metric for the B-to-A transition. The calculations reveal that in the presence of a SWNT DNA favors B-form DNA significantly in both poly-GC and poly-AT sequences. Furthermore, the poly-AT DNA:SWNT complex shows a higher energy penalty for adopting an A-like conformation than poly-GC DNA:SWNT by several kcal/mol. The presence of a SWNT on either poly-AT or poly-GC DNA affects the PMF of the transition such that the B form is favored by as much as 10 kcal/mol. In agreement with published data, we find a potential energy minimum between A and B-form DNA at ΔRMSD ≈ -1.5 Å and that the presence of the SWNT moves this minimum by as much as ΔRMSD = 3 Å.
Project description:We report the construction of DNA nanotubes covalently functionalized with the cell adhesion peptide RGDS as a bioactive substrate for neural stem cell differentiation. Alteration of the Watson-Crick base pairing program that builds the nanostructures allowed us to probe independently the effect of nanotube architecture and peptide bioactivity on stem cell differentiation. We found that both factors instruct synergistically the preferential differentiation of the cells into neurons rather than astrocytes.
Project description:The differences in effectiveness of multi-walled carbon nanotubes (MWCNTs) as the dispersive solid-phase extraction (dSPE) sorbent for the selective extraction of polycyclic aromatic hydrocarbons (PAHs) were explained on the basis of theoretical study. It was observed that for low molecular weight PAHs, the recoveries using non-helical and helical MWCNTs were similar. In contrary, for PAHs containing five or more aromatic rings, the extraction efficiency was higher using HMWCNTs than for non-helical ones. Principle component analysis (PCA) as well as providing structural parameters and interaction energies for adsorption processes (PAH + CNT ? PAH-CNT) have been used for this purpose. All the PAH + CNT???PAH-CNT adsorption processes considered were found to be thermodynamically favorable. However, the adsorption energies (Eads) for PAHs and the helical carbon nanotube surface estimated for the B(a)P-HCNT and I(1,2,3-cd)P-HCNT are substantially less negative than those observed for PAH molecules interacting with the non-helical CNT. Namely, the Eads calculated in simulated aqueous environment for the B(a)P-MWCNT(6,2) and I(1,2,3-cd)P-MWCNT(6,2) were respectively -?43.32 and -?59.98 kcal/mol, while values of only -?7.75 kcal/mol (B(a)P-HCNT) and -?9.13 kcal/mol (I(1,2,3-cd)P-HCNT) were found for the corresponding PAH-HCNT systems. Therefore, we conclude that the replacement of MWCNTs with HCNTs leads to PAH-HCNT systems in which the interaction energies are much smaller than those estimated for the corresponding PAH-MWCNT systems. HMWCNTs are therefore recommended as the dSPE sorbent phase for the extraction of both low and high molecular weight PAHs from water samples.
Project description:Carbon nanotubes internalize into cells and are potential molecular platforms for siRNA and DNA delivery. A comprehensive understanding of the identity and stability of ammoniumfunctionalized carbon nanotube (f-CNT)-based nucleic acid constructs is critical to deploying them in vivo as gene delivery vehicles. This work explored the capability of f-CNT to bind single- and double-strand oligonucleotides by determining the thermodynamics and kinetics of assembly and the stoichiometric composition in aqueous solution. Surprisingly, the binding affinity of f-CNT and short oligonucleotide sequences was in the nanomolar range, kinetics of complexation were extremely rapid, and from one to five sequences were loaded per nanotube platform. Mechanistic evidence for an assembly process that involved electrostatic, hydrogen-bonding and ?-stacking bonding interactions was obtained by varying nanotube functionalities, oligonucleotides, and reaction conditions. 31P-NMR and spectrophotometric fluorescence emission data described the conditions required to assemble and stably bind a DNA or RNA cargo for delivery in vivo and the amount of oligonucleotide that could be transported. The soluble oligonucleic acid-f-CNT supramolecular assemblies were suitable for use in vivo. Importantly, key evidence in support of an elegant mechanism by which the bound nucleic acid material can be 'off-loaded' from the f-CNT was discovered.
Project description:Ca2+ (1-5 mM) and lanthanide (20-250 microM) ions enhance the rate of polymerization of purified calf skin collagen (1.5 mg/ml) at pH 7.0 in the presence of 30mM-Tris/HCl and 0.2 M-NaCl. Both the nucleation phase and the growth phase of polymerization are accelerated. The activation energy of the growth phase, 239.3 +/- 24.3 kJ/mol (57.2 +/- 5.8 kcal/mol), is decreased to 145.6 +/- 9.6 kJ/mol (34.8 +/- 2.3 kcal/mol) by 5 mM-Ca2+ and to 75.3 +/- 4.6 kJ/mol (18.0 +/- 1.1 kcal/mol) by 25 microM-Sm3+. In contrast, the activation energy of the nucleation phase, 191.6 +/- 23.4 kJ/mol (45.8 +/- 5.6 kcal/mol), is only slightly decreased by Ca2+ or Sm3+. Collagen fibrils formed in the presence of Sm3+ are thinner than control fibrils, and more thermoresistant.
Project description:The authors report a method where in-situ photon assisted heating of multi-wall carbon nanotubes was utilized for enhanced polymerization of the nanotube/polydimethylsiloxane interface that resulted in significant load transfer and improved mechanical properties. Large Raman shifts (20 cm(-1) wavenumbers) of the 2D bands were witnessed for near-infrared light polymerized samples, signifying increased load transfer to the nanotubes for up to ∼80% strains. An increase in elastic modulus of ∼130% for 1 wt. % composites is reported for photon assisted crosslinking.
Project description:Carbon nanotubes are a promising platform across a broad spectrum of applications ranging from separations technology, drug delivery, to bio(electronic) sensors. Proper dispersion of carbon nanotube materials is important to retaining the electronic properties of nanotubes. Experimentally it has been shown that salts can regulate the dispersing properties of CNTs in aqueous system with surfactants (Niyogi, S.; Densmore, C. G.; Doorn, S. K. J. Am. Chem. Soc.2009, 131, 1144-1153); details of the physicochemical mechanisms underlying such effects continue to be explored. We address the effects of inorganic monovalent salts (NaCl and NaI) on dispersion stability of carbon nanotubes.We perform all-atom molecular dynamics simulations using nonpolarizable interaction models to compute the potential of mean force between two (10,10) single-walled carbon nanotubes (SWNTs) in the presence of NaCl/NaI and compare to the potential of mean force between SWNTs in pure water. Addition of salts enhances stability of the contact state between two SWNT's on the order of 4 kcal/mol. The ion-specific spatial distribution of different halide anions gives rise to starkly different contributions to the free energy stability of nanotubes in the contact state. Iodide anion directly stabilizes the contact state to a much greater extent than chloride anion. The enhanced stability arises from the locally repulsive forces imposed on nanotubes by the surface-segregated iodide anion. Within the time scale of our simulations, both NaI and NaCl solutions stabilize the contact state by equivalent amounts. The marginally higher stability for contact state in salt solutions recapitulates results for small hydrophobic solutes in NaCl solutions (Athawale, M. V.; Sarupria, S.; Garde, S. J. Phys. Chem. B2008, 112, 5661-5670) as well as single-walled carbon nanotubes in NaCl and CaCl2 aqueous solutions.