Project description:The transmembrane protein ?-hemolysin pore has been used to develop ultrasensitive biosensors, study biomolecular folding and unfolding, investigate covalent and noncovalent bonding interactions, and probe enzyme kinetics. Here, we report that, by addition of ionic liquid tetrakis(hydroxymethyl)phosphonium chloride solution to the ?-hemolysin pore, the ?-hemolysin channel can be controlled open or closed by adjusting the pH of the solution. This approach can be employed to develop a novel molecular switch to regulate molecular transport and should find potential applications as a "smart" drug delivery method.
Project description:DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.
Project description:26Al-26Mg ages were determined for 14 anorthite-bearing chondrules from five different unequilibrated ordinary chondrites (UOCs) with low petrologic subtypes (3.00-3.05). In addition, oxygen three isotopes of these chondrules were also measured. The selected chondrules are highly depleted in alkali elements, and anorthite is the only mesostasis phase, though they show a range of mafic mineral compositions (Mg# 76-97 mole%) that are representative of chondrules in UOCs. The mean ∆17O values in these chondrules range from -0.44 ± 0.23‰ to 0.49 ± 0.15‰, in good agreement with previous studies of plagioclase-bearing chondrules from UOCs. Anorthite in all chondrules exhibit resolvable excess 26Mg (> 1.0 ± 0.4‰). Their inferred (27Al/26Al)0 range from (6.3 ± 0.7)×10-6 to (8.9 ± 0.3)×10-6 corresponding to a timescale for chondrule formation of 1.8 ± 0.04 Ma to 2.16 ± 0.12/0.11 Ma after CAIs using a canonical (27Al/26Al)0 value of 5.25×10-5. The ages from six chondrules in LL chondrites are restricted to between 1.8 Ma and 1.9 Ma, whereas eight chondrules in L chondrites show ages from 1.8 Ma to 2.2 Ma, including three chondrules at ~2.0 Ma and two chondrules at ~2.15 Ma. The inferred chondrule formation ages from this study are at the peak of those previously determined for UOC chondrules, though with much shorter durations. This is potentially due to the time difference between formation of anorthite-bearing chondrules and typical UOC chondrules with alkali-rich compositions. Alternatively, younger chondrules ages in previous studies could have been the result of disturbance to the Al-Mg system in glassy mesostasis even at the low degree of thermal metamorphism in the parent bodies. Nevertheless, the high precision ages from this study (with uncertainties from 0.04 Ma to 0.15 Ma) indicate that there was potentially more than one chondrule forming event represented in the studied population. Considering data from LL chondrites only, the restricted duration (≤0.1 Ma) of chondrule formation ages suggests an origin in high density environments that subsequently lead to parent body formation. However, the unusually low alkali contents of the studied chondrules compared to common alkali-rich chondrules could also represent earlier chondrule formation events under relatively lower dust densities in the disk. Major chondrule forming events for UOCs might have postdated or concurrent with the younger anorthite-bearing chondrule formation at 2.15 Ma after CAIs, which are very close to the timing of accretion of ordinary chondrite parent bodies that are expected from thermal evolution of ordinary chondrite parent bodies.
Project description:The synthesis of a peptide-containing lasso molecular switch by a self-entanglement strategy is described. The interlocked rotaxane molecular machine consists of a benzometaphenylene[25]crown-8 (BMP25C8) macrocycle surrounding a molecular axle. This molecular axle contains a tripeptidic sequence and two molecular stations: a N-benzyltriazolium and a pH-sensitive anilinium station. The tripeptide is located between the macrocycle and the triazolium station, so that its conformation can be tailored depending on the shuttling of the macrocycle from one station to the other. At acidic pH, the macrocycle resides around the anilinium moiety, whereas it shuttles around the triazolium station after deprotonation. This molecular machinery thus forces the lasso to adopt a tightened or a loosened conformation.
Project description:Aptamers that recognize specific cells in a complex environment have emerged as invaluable molecular tools in bioanalysis and in the development of targeted therapeutics. The selective recognition of aptamers, however, can be compromised by the coexistence of target receptors on both target cells and other cells. To address this problem, we constructed a structure-switchable aptamer (SW-Apt) with reconfigurable binding affinity in accordance with the microenvironment of target cells. The SW-Apt makes use of i-motifs, which are quadruplex structures that form in sequences rich in cytosine. More specifically, we report the design of single-stranded, pH-responsive i-motif-modified aptamers able to bind specifically with target cells by exploiting their pH. Here, the i-motif serves as a structural domain to either facilitate the binding ability of aptamers to target cells or suppress the binding ability of aptamers to nontarget cell based on the pH of the cellular microenvironment. SW-Apt exhibited high binding ability with target cells at acidic pH, while no obvious binding was observed at physiological pH. The i-motif-induced structure-switching was verified with Förster resonance energy transfer and circular dichroism spectroscopy. Notably, SW-Apt exhibits high specificity in serum and excellent stability, likely attributed to the folded quadruplex i-motif structure. This study provides a simple and efficient strategy to chemically modulate aptamer binding ability and thus improve aptamer binding specificity to target cells, irrespective of the coexistence of identical receptors on target and nontarget cells.
Project description:We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the fuel acids to a water solution initially causes a rapid transient pH decrease, which is then followed by a slower pH increase. We have employed such low-to-high pH cycles to control in a dissipative way the operation of two model DNA-based nanodevices: a DNA nanoswitch undergoing time-programmable open-close-open cycles of motion, and a DNA-based receptor able to release-uptake a DNA cargo strand. The kinetics of the transient operation of both systems can be easily modulated by varying the concentration of the acid fuel added to the solution and both acid fuels show an efficient reversibility which further supports their versatility.
Project description:New methods for the preparation of reversible pH-responsive DNA hydrogels based on Hoogsteen triplex structures are described. One system consists of a hydrogel composed of duplex DNA units that bridge acrylamide chains at pH = 7.4 and undergoes dissolution at pH = 5.0 through the reconfiguration of one of the duplex bridging units into a protonated CG·C+ triplex structure. The second system consists of a hydrogel consisting of acrylamide chains crosslinked in the presence of an auxiliary strand by Hoogsteen TA·T triplex interaction at pH = 7.0. The hydrogel transforms into a liquid phase at pH = 10.0 due to the separation of the triplex bridging units. The two hydrogel systems undergo reversible and cyclic hydrogel/solution transitions by subjecting the systems to appropriate pH values. The anti-cancer drug, coralyne, binds specifically to the TA·T triplex-crosslinked hydrogel thereby increasing its stiffness. The pH-controlled release of the coralyne from the hydrogel is demonstrated.
Project description: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.
Project description:GCAP1 is a neuronal calcium sensor protein that regulates the phototransduction cascade in vertebrates by switching between activator and inhibitor of the target guanylate cyclase (GC) in a Ca2+-dependent manner. We carried out exhaustive molecular dynamics simulations of GCAP1 and determined the intramolecular communication pathways involved in the specific GC activator/inhibitor switch. The switch was found to depend on the Mg2+/Ca2+ loading states of the three EF hands and on the way the information is transferred from each EF hand to specific residues at the GCAP1/GC interface. Post-translational myristoylation is fundamental to mediate long range allosteric interactions including the EF2-EF4 coupling and the communication between EF4 and the GC binding interface. Some hubs in the identified protein network are the target of retinal dystrophy mutations, suggesting that the lack of complete inhibition of GC observed in many cases is likely due to the perturbation of intra/intermolecular communication routes.
Project description:In this work we synthesize molecular switches that are responsive to cysteine, homocysteine, and glutathione; three redox systems that make up the majority of the body's antioxidant defenses. Synthesized spiropyran isomers with conjugation-ready linkages showed good selectivity of response to these major antioxidant thiols over nucleophilic amino acids; however the position of the linking group can affect selectivity and reversibility of the switching response. An isomer with selectivity for cysteine against GSH and Hcy was identified.