Chemically synthesized zinc finger molecules as nano-addressable probes for double-stranded DNAs

Our experiments describe an alternative method of dsDNA recognition using zinc finger (ZF) molecules which bind DNA specifically and with high affinity. Our aim was to develop zinc finger probes which are able to bind to dsDNA molecules at predetermined sites. In our basic approach we used pairs of complementary oligonucleotides to form dsDNAs, containing one of the three SP1-transcription factor motifs as a zinc finger recognition site. Two zinc finger probes of the SP1 motif were chemically synthesized and modified with a Dy-633 fluorophore. The SP1 peptides were folded into functional zinc fingers using zinc chloride. The addressable dsDNAs were immobilized on optical fibres, and the kinetics and binding rates of the artificial zinc finger probes were measured by a fluorescence detecting device (photomultiplying tube). The two zinc fingers and their corresponding DNA recognition sites served as specific probes and controls for the matching site and vice versa. Our experiments showed that a variety of dsDNA-binding probes may be created by modification of the amino acid sequence of natural zinc finger proteins. Our findings offer an alternative approach of addressing dsDNA molecules, for example for use in a nanoarray device

Echtzeitdetektion von Punktmutationen mit DNA-Chips am Beispiel des SULT1A1*213-SNP

Der Identifizierung von Punktmutationen im menschlichen Genom kommt eine hohe Bedeutung zu. Die Entdeckung einer Vielzahl von SNPs ('single nucleotide polymorphisms'), also Mutationen einzelner Basen, die definitionsgemäß bei mehr als 1% der Bevölkerung auftreten, und die Erkenntnis, dass SNPs die Nebenwirkungen von Medikamenten determinieren können, führte zu der Vision einer 'personalisierten Medizin': Der Patient erhält nach einer Genotypisierung das für ihn verträglichste Medikament verschrieben. Notwendige Bedingung für das neue Paradigma ist eine schnelle und hochdurchsatzfähige DNA-Analytik. Da bis zu 3 Millionen von SNPs beim Menschen vermutet werden (www.snp.cshl.org), ist das etablierte Verfahren mittels PCR-Amplifikation, Restriktionsenzymverdau und Elektrophorese nicht praktikabel. Neben den zum Massenscreening geeigneten, spezialisierten MALDI- (z.B. Sequenom ®) und Primer-Extension-Verfahren (z.B. Orchid Biocomputer ®) wird insbesondere die DNA-Chip-Technologie als vielversprechende Methode für mittlere bis hohe Durchsätze und Vor-Ort-Anwendungen angesehen. Der Einsatz dieses Verfahrens zum SNP-Screening wird am Beispiel des SULT1A1*213-SNPs demonstriert. Das SULT1A1-Gen beim Menschen kodiert für eine cytosolische, thermostabile Phenol-Sulfotransferase (P-PST, EC 2.8.2.1), die in der Leber durch Sulfonierung von phenolischen Substraten Biosynthese und Entgiftungsfunktionen ausübt. Bisher wurden drei Punktmutationen in diesem Gen entdeckt (Raftogianis 1997). Die Variation *213Arginin nach *213Histidin, die bei ca. 37% der (kaukasischen) Bevölkerung auftritt, führt zu einem deutlich verschiedenen Phänotyp (geringere Aktivität, geringere Thermostabilität, Engelke 2000) und wird mit Übergewicht in Zusammenhang gebracht

Microscopic understanding of heavy-tailed return distributions in an agent-based model

The distribution of returns in financial time series exhibits heavy tails. In empirical studies, it has been found that gaps between the orders in the order book lead to large price shifts and thereby to these heavy tails. We set up an agent based model to study this issue and, in particular, how the gaps in the order book emerge. The trading mechanism in our model is based on a double-auction order book, which is used on nearly all stock exchanges. In situations where the order book is densely occupied with limit orders we do not observe fat-tailed distributions. As soon as less liquidity is available, a gap structure forms which leads to return distributions with heavy tails. We show that return distributions with heavy tails are an order-book effect if the available liquidity is constrained. This is largely independent of the specific trading strategies

Integrated planar optical waveguide interferometer biosensors: A comparative review

Integrated planar optical waveguide interferometer biosensors are advantageous combinations of evanescent field sensing and optical phase difference measurement methods. By probing the near surface region of a sensor area with the evanescent field, any change of the refractive index of the probed volume induces a phase shift of the guided mode compared to a reference field typically of a mode propagating through the reference arm of the same waveguide structure. The interfering fields of these modes produce an interference signal detected at the sensor׳s output, whose alteration is proportional to the refractive index change. This signal can be recorded, processed and related to e.g. the concentration of an analyte in the solution of interest. Although this sensing principle is relatively simple, studies about integrated planar optical waveguide interferometer biosensors can mostly be found in the literature covering the past twenty years. During these two decades, several members of this sensor family have been introduced, which have remarkably advantageous properties. These entail label-free and non-destructive detection, outstandingly good sensitivity and detection limit, cost-effective and simple production, ability of multiplexing and miniaturization. Furthermore, these properties lead to low reagent consumption, short analysis time and open prospects for point-of-care applications. The present review collects the most relevant developments of the past twenty years categorizing them into two main groups, such as common- and double path waveguide interferometers. In addition, it tries to maintain the historical order as it is possible and it compares the diverse sensor designs in order to reveal not only the development of this field in time, but to contrast the advantages and disadvantages of the different approaches and sensor families, as well