Exotic kinetic phenomena and their chemical explanation in the iodate-sulfite-thiosulfate system

Rábai, Gyula; Beck, M. T.

doi:10.1021/j100321a021

Cited by 41 publications

(46 citation statements)

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“…In fact, these spikes also occur experimentally, but their short duration (t 1/2 % 2 s) means they cannot be resolved by our pH meter, which has a response time of 30 s. We independently checked the occurence of the spikes at low pH values with the pH-sensitive dye methyl orange, which changes its color from yellow to pink at pH 4.4. [10] Indeed, during the operation of the oscillator we observed this color change for fractions of a second at the position of the low pH spikes. This also explains why we observe fluorescence values at the minima of the pH oscillations which are lower than those expected from the recorded pH values.…”

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confidence: 80%

“…Simulated time traces of the pH oscillations based on a model developed by Rabai and Beck [10] are also shown in Figure 3. Experimentally obtained data agree well with the models prediction at pH values above 5.5.…”

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confidence: 99%

“…Top: The surface-bound i motif unfolds at 37 8C, while a surface-bound control strand does not show any change in fluorescence. Bottom: For the experiment in solution, the i motif strand labeled with a dye on one end and a quencher on the other end [10] displays essentially the same behavior and unfolds at a slightly higher temperature than on the surface. The control strand exhibits only a small change in the fluorescence in the solution experiment.…”

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confidence: 99%

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A Surface‐Bound DNA Switch Driven by a Chemical Oscillator

2006

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The fabrication of autonomously moving molecular structures is one of the central challenges in the field of DNA nanodevices.[1] Some of the concepts introduced recently to achieve this goal rely on the sequence-dependent catalytic action of DNA-modifying enzymes such as restriction endonucleases or nicking enzymes [2] while others use the catalytic power of DNA itself by incorporating DNA enzyme sequences into DNA devices.[3] Both approaches have also been used to realize autonomous molecular computers.[4] Another strategy is based on controlled inhibition of DNA hybridization by formation of secondary structure and its acceleration by catalytic DNA strands.[5] These concepts were developed for the autonomous operation of DNA devices fueled by DNA hybridization. A different approach was recently taken by our research group [6] and we could show that the pH-sensitive conformational transition of a cytosinerich DNA strand between a random conformation and the socalled "i motif" could be driven by the oscillating proton concentration generated by a chemical oscillator. In such a system, the temporal succession of the states of the DNA devices is determined by a nonlinear dynamical system rather than by an external operator. We report here how this system can be significantly improved by attaching the DNA conformational switches to a solid substrate. This attachment allows us to operate the chemical oscillator in a continuous flow stirred tank reactor (CSTR) into which a glass chip supporting the DNA devices is placed. In principle, the surface-bound DNA structures can undergo an infinite number of autonomous conformational switching events in this configuration.We showed recently how proton-fueled DNA devices can be driven by an oscillating chemical reaction [6] by using a variant of the Landolt reaction to periodically change the pH value in a continuously fed reactor. To retain the DNA switches within the reaction solution, a reactor without an outlet had to be used. In such a configuration, one cannot reach a steady state since the continuous influx of reaction solution means the average concentrations of the reactants vary. As a result, this dynamic chemical system is driven out of its oscillatory region, thus causing the oscillations to die away after a few periods.To overcome this limitation in the present work we operated the oscillator in a CSTR with two inlets and one outlet. In principle, an infinite number of homogeneous pH oscillations can be generated by using a continuous filling combined with the simultaneous removal of waste materials. However, the DNA devices had to be attached to a solid substrate to prevent loss of the DNA through the reactors outlet. For these experiments, we used thiol-modified, fluorescently labeled DNA switches bound to an ultrathin transparent gold layer on a glass substrate. This allowed a firm covalent attachment of the DNA to the surface while at the same time energy transfer between the fluorophores and the gold layer [7] could be used to characterize the conformational...

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confidence: 80%

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confidence: 99%

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confidence: 99%

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A Surface‐Bound DNA Switch Driven by a Chemical Oscillator

2006

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“…The reaction was initiated by adding 1. were quenched by acidified sulfite solution to prevent the reduction of IO 3 − by sulfite [3,23]. Aliquot fractions for the analysis of HOI and I 2 were quenched by high excess of phenol [12,24].…”

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confidence: 99%

“…Aliquots of the reacted solution were withdrawn and added acidified sulfite solution ([HSO 3 − ]:[MnO 4 − ] = 1.3-2) to quench the remaining potassiumpermanganate[3,23].…”

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confidence: 99%