Predictive Value of a Model of the Briggs−Rauscher Reaction Fitted to Quenching Experiments

Vukojević, Vladana; Sørensen, and P. Graae; Hynne, F.

doi:10.1021/jp960785o

Cited by 48 publications

(59 citation statements)

References 15 publications

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“…Numerical simulations were carried out using the Gepasi 3.30 software package for modeling biochemical systems (36) and software for numerical integration of kinetic equations with the fifth order Runge Kutta method (37).…”

Section: Methodsmentioning

confidence: 99%

Quantitative study of synthetic Hox transcription factor–DNA interactions in live cells

Vukojević

Papadopoulos²,

Terenius³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Transcription factor-DNA interactions are life sustaining and therefore the subject of intensive research. In spite of vast effort, quantitative in vivo studies of the molecular mechanisms underlying these fundamental interactions remain challenging. In the preceding paper, we designed synthetic Sex combs reduced (Scr) peptides and validated genetically their function as transcriptional regulators. Here we present a controllable system for quantitative studies of protein-DNA interactions in live cells that enables us to "titrate" the concentration of the synthetic Scr peptides in a single cell. Using methods with single-molecule sensitivity, advanced fluorescence imaging and fluorescence correlation spectroscopy (FCS), we were able to study the kinetics of Scr-DNA interactions in live salivary gland cells, where Scr is normally expressed during development. We discerned freely moving Scr molecules, characterized the specific and nonspecific Scr peptide-DNA interactions, and estimated their corresponding dissociation constants (K d ) in vivo. Our results suggest that the synthetic Scr transcription factors find their specific target sites primarily by multiple association/dissociation events, the rapidity of which is largely owed to electrostatic interactions. Based on these new findings, we formulate a model mechanism and emulate the kinetics of Scr homeodomain-DNA interactions in live cells using numerical simulations.fluorescence correlation spectroscopy | single-molecule sensitivity | homeodomain | Sex combs reduced | synthetic peptides T ranscription factor-DNA interactions, the assembly of functional transcriptional complexes, and the mechanisms involved in target site recognition are central to understanding gene regulation in vivo. In spite of such relevance, kinetic studies of transcription factor-DNA interactions are limited and have been performed only for a handful of proteins. Most prominent studies include the lac repressor in Escherichia coli (1-4), nuclear receptor-directed transcription (5), helicase translocation along DNA (6), and restriction enzymes-DNA interactions (7,8). The majority of these studies are carried out with naked DNA or reconstituted chromatin, reflecting the in vivo situation only to a limited extent. Chromatin structure in live cells is highly dynamic, involving multiple interactions and transformations (9)(10)(11). Moreover, a number of cofactors and coactivators/corepressors are involved in transcriptional regulation, suggesting that gene expression is accomplished through a dynamic, spatiotemporally entangled interplay between concomitant processesprotein searching for specific target sites, rearrangements of DNA conformation, and recruitment of cofactors and/or coregulators (5, 12, 13). Such complexity is not easily mimicked in solution, therefore necessitating live cell experimentation. However, these measurements are complex, and kinetic studies of protein-DNA interactions in live cells remain scarce (3,4,14,15), mainly due to the limited number of experimental approach...

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Section: Methodsmentioning

confidence: 99%

Quantitative study of synthetic Hox transcription factor–DNA interactions in live cells

Vukojević

Papadopoulos²,

Terenius³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…The Briggs–Rauscher (BR) oscillating reaction 1 has received growing attention in recent years not only for the attempt to elucidate its complex mechanism 2, 3 but also for the inhibitory effects by antioxidants on the oscillatory regime. These inhibitory effects permit precise, rapid, and inexpensive measurements of the relative activity of substances which are scavengers of free radicals 4, 5.…”

Section: Introductionmentioning

confidence: 99%

Benzylmalonic acid reaction with iodine and behavior in a Briggs–Rauscher oscillator

Cervellati

Furrow

Pompeis

2002

Int J of Chemical Kinetics

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Benzylmalonic acid (BzMA) reacts via an enol mechanism with aqueous iodine to form rather stable iodobenzylmalonic acid. In the presence of iodate, which oxidizes iodide to di‐iodine, the reaction goes to completion. The kinetics of the reaction BzMA + I2 + IO3− + H+ have been studied and the results were interpreted with a suitable mechanism. In a mixture with acidic iodate, hydrogen peroxide, and manganous ions, BzMA can serve as a substrate for a Briggs–Rauscher‐type oscillating reaction. The behavior of this oscillator has been studied in detail. A mechanistic interpretation of the oscillations based on a new kinetic model is also given. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 357–365, 2002

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“…Otkad je otkrivena 1972. god. [24], Brigs-Raušer reakcija privlači veliku pažnju kako zbog ispitivanja samog mehanizma reakcije [25][26][27], tako i zbog egzotične dinamike koju ispoljava [28,29].…”

Section: Uvodunclassified

Oscillatory reaction as a system detector for doped and undoped phosphate tungsten bronzes

Maksimović

Joksović

et al. 2018

Hem Ind

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Phosphate tungsten bronzes, obtained by thermal treatment, are insufficiently investigated bronzes and there is scarce literature data on their chemical behavior and structure. Due to high-sensitivity of the Briggs-Rauscher (BR) reaction to addition of different analytes, this oscillatory reaction presents a potentially important chemical system for investigation and characterization of phosphate-tungsten bronzes, doped and undoped. The reaction mixture for the oscillatory BR reaction typically consists of H2O2, HClO4, KIO3, Mn(II) (catalyst), and CH2(COOH)2 (malonic acid, as an organic substrate). This paper deals with phosphate tungsten bronzes (PWB) and lithium doped phosphate tungsten bronzes (LiPWB) and their effects on the Briggs-Rauscher reaction dynamics. It is shown that the addition of phosphate tungsten bronzes decreases the oscillatory period length in this reaction. Furthermore, the obtained results show that PWB has a stronger influence on the BR reaction dynamics then LiPWB. In both cases, the oscillatory period is a linear function of the added bronze mass. The obtained linear functions can be successfully used for determination of the unknown bronze mass. Furthermore, due to different slopes of these functions, the Briggs-Rauscher reaction can be used as a system-detector for lithium doped and undoped phosphate tungsten bronzes. In order to elucidate the mechanism of bronze action, the inductively coupled plasma optical emission spectrometry (ICP-OES) was used to measure the total contents of K, Mn, W, Li. The aliquots of the above solution (i.e. CH2(COOH)2, MnSO4, HClO4, KIO3 but without H2O2) with the identical masses of PWB and LiPWB were examined. For the sake of comparison, contents of the metals in the solution without the bronze addition were measured, as well. Results obtained by the ICP-OES analysis show that the bronze structure is disturbed in the strong oxidizing environment (iodate in acidic solution) so that both, tungsten and lithium, leach into the BR solution. Accordingly, the proposed mechanism of the bronze action is probably by the reaction of tungsten ion with hydrogen-peroxide resulting in formation of a tungsten-peroxo complex. This complex is a stronger oxidizing agent then hydrogen peroxide itself. Thus, formation of the tungsten-peroxo complex potentially affects the kinetics of the Briggs-Rauscher reaction. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. 172015, Grant no. III45001 and Grant no. III45014]

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Predictive Value of a Model of the Briggs−Rauscher Reaction Fitted to Quenching Experiments

Cited by 48 publications

References 15 publications

Quantitative study of synthetic Hox transcription factor–DNA interactions in live cells

Quantitative study of synthetic Hox transcription factor–DNA interactions in live cells

Benzylmalonic acid reaction with iodine and behavior in a Briggs–Rauscher oscillator

Oscillatory reaction as a system detector for doped and undoped phosphate tungsten bronzes

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