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Striedner Y.,Johannes Kepler University | Schwarz T.,Johannes Kepler University | Welte T.,Dynamic Biosensors GmbH | Futschik A.,Johannes Kepler University | And 2 more authors.
Chromosome Research | Year: 2017

PR domain containing protein 9 (PRDM9) is a meiosis-specific, multi-domain protein that regulates the location of recombination hotspots by targeting its DNA recognition sequence for double-strand breaks (DSBs). PRDM9 specifically recognizes DNA via its tandem array of zinc fingers (ZnFs), epigenetically marks the local chromatin by its histone methyltransferase activity, and is an important tether that brings the DNA into contact with the recombination initiation machinery. A strong correlation between PRDM9-ZnF variants and specific DNA motifs at recombination hotspots has been reported; however, the binding specificity and kinetics of the ZnF domain are still obscure. Using two in vitro methods, gel mobility shift assays and switchSENSE, a quantitative biophysical approach that measures binding rates in real time, we determined that the PRDM9-ZnF domain forms a highly stable and long-lived complex with its recognition sequence, with a dissociation halftime of many hours. The ZnF domain exhibits an equilibrium dissociation constant (KD) in the nanomolar (nM) range, with polymorphisms in the recognition sequence directly affecting the binding affinity. We also determined that alternative sequences (15–16 nucleotides in length) can be specifically bound by different subsets of the ZnF domain, explaining the binding plasticity of PRDM9 for different sequences. Finally, longer binding targets are preferred than predicted from the numbers of ZnFs contacting the DNA. Functionally, a long-lived complex translates into an enzymatically active PRDM9 at specific DNA-binding sites throughout meiotic prophase I that might be relevant in stabilizing the components of the recombination machinery to a specific DNA target until DSBs are initiated by Spo11. © 2017 The Author(s)


Clery A.,ETH Zurich | Sohier T.J.M.,ETH Zurich | Welte T.,Dynamic Biosensors GmbH | Langer A.,Dynamic Biosensors GmbH | Allain F.H.T.,ETH Zurich
Methods | Year: 2017

Characterization of RNA-binding protein interactions with RNA became inevitable to properly understand the cellular mechanisms involved in gene expression regulation. Structural investigations bring information at the atomic level on these interactions and complementary methods such as Isothermal Titration Calorimetry (ITC) and Surface Plasmon Resonance (SPR) are commonly used to quantify the affinity of these RNA-protein complexes and evaluate the effect of mutations affecting these interactions. The switchSENSE technology has recently been developed and already successfully used to investigate protein interactions with different types of binding partners (DNA, protein/peptide or even small molecules). In this study, we show that this method is also well suited to study RNA binding proteins (RBPs). We could successfully investigate the binding to RNA of three different RBPs (Fox-1, SRSF1 and Tra2-β1) and obtained KD values very close to the ones determined previously by SPR or ITC for these complexes. These results show that the switchSENSE technology can be used as an alternative method to study protein-RNA interactions with KD values in the low micromolar (10-6) to nanomolar (10-7-10-9) and probably picomolar (10-10-10-12) range. The absence of labelling requirement for the analyte molecules and the use of very low amounts of protein and RNA molecules make the switchSENSE approach very attractive compared to other methods. Finally, we discuss about the potential of this approach in obtaining more sophisticated information such as structural conformational changes upon RBP binding to RNA. © 2017.


The present invention relates to a combination product which can be used to detect and/or characterize interactions between two molecules, in particular two proteins and most particular between an antigen and an antibody. The combination product comprises a nucleic acid structure comprising a double-stranded part and a single- stranded part which is capable of hybridizing to another single-stranded nucleic acid molecule which is also part of the combination product.


The present invention relates to a method of identifying a nucleotide at a defined position and determining the sequence of a target polynucleotide using an electro-switchable biosensor, as well as devices comprising an electro-switchable biosensor and uses thereof.


Patent
Dynamic Biosensors GmbH | Date: 2014-01-22

The present invention is directed to sequencing of nucleic acids. A method is provided for sequencing based on immobilized nucleic acid on a surface. Advantageously, a long range detection mechanism is used for detecting, whether a nucleotide provided to the substrate of a biochip has been incorporated into the immobilized template nucleic acid. Various different alignment means are provided by the present invention which can be used for facilitating a rigidly locking of the orientation of the DNA complex, which complex comprises the template nucleic acid, the primer and the capture nucleic acid. Various different linker systems may be used to immobilize the DNA complex at a first and a second strand end, such that the desired alignment of the DNA complex is achieved. Also co-adsorbed molecules on the substrate surface can be used for such an aligning measure. Additionally, or alternatively, an electrical field may be applied for repelling the DNA complex from the electrode and for facilitating a vertical DNA complex orientation. Advantageously, label-free nucleotides can be used, if desired.


Patent
Dynamic Biosensors GmbH | Date: 2015-09-17

Arrangements are described for evaluating characteristics of target molecules. A biochip is received which includes a substrate to which charged probe molecules are attached. The probe molecules have a marker to allow generating signals indicative of the distance of a portion of the probe molecule from the substrate. The signals are detected and means for an external electric field is generated to which the probe molecules are exposed. A control means acts to: (A) apply an external electric field causing the portion of the probe molecule to approach the substrate, and (B) apply an external electric field causing the portion of the probe molecule to move away from the substrate. The signal is recorded as a function of time during step (A) and/or step (B). Steps (A) and (B) are repeated for a predetermined number of times and the recorded signals are combined.


PubMed | University of Sussex and Dynamic Biosensors GmbH
Type: | Journal: Nature communications | Year: 2017

The Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin and Smc5/6 are involved in the organization of higher-order chromosome structure-which is essential for accurate chromosome duplication and segregation. Each complex is scaffolded by a specific SMC protein dimer (heterodimer in eukaryotes) held together via their hinge domains. Here we show that the Smc5/6-hinge, like those of cohesin and condensin, also forms a toroidal structure but with distinctive subunit interfaces absent from the other SMC complexes; an unusual molecular latch and a functional hub. Defined mutations in these interfaces cause severe phenotypic effects with sensitivity to DNA-damaging agents in fission yeast and reduced viability in human cells. We show that the Smc5/6-hinge complex binds preferentially to ssDNA and that this interaction is affected by both latch and hub mutations, suggesting a key role for these unique features in controlling DNA association by the Smc5/6 complex.


Trademark
Dynamic Biosensors GmbH | Date: 2014-02-06

Biosensors; analysers; testing apparatus not for medical purposes; optical sensors; electro-optical sensors; electronic sensors; photo-electric sensors. Apparatus for use in medical analysis; testing apparatus for medical purposes; immunological analysers; physical analysers for medical use; haematology analysers. Research relating to biotechnology; research in the field of biotechnology; scientific research in the field of medicine.


This report studies Biochip Products in Global Market, especially in North America, Europe, China, Japan, Korea and Taiwan, focuses on top manufacturers in global market, with production, price, revenue and market share for each manufacturer, covering  Illumina  Thermo Fisher Scientific  Cellix  GE Healthcare  Randox  BioDot  PerkinElmer  Roche  Horiba  Greiner Bio One International  Korea Materials & Analysis  Capitalbio  Dynamic Biosensors Market Segment by Regions, this report splits Global into several key Regions, with production, consumption, revenue, market share and growth rate of Biochip Products in these regions, from 2011 to 2021 (forecast), like  North America  Europe  China  Japan  Korea  Taiwan  Split by product type, with production, revenue, price, market share and growth rate of each type, can be divided into  Type I  Type II  Type III  Split by application, this report focuses on consumption, market share and growth rate of Biochip Products in each application, can be divided into  Application 1  Application 2  Application 3 Global Biochip Products Market Research Report 2016  1 Biochip Products Market Overview  1.1 Product Overview and Scope of Biochip Products  1.2 Biochip Products Segment by Type  1.2.1 Global Production Market Share of Biochip Products by Type in 2015  1.2.2 Type I  1.2.3 Type II  1.2.4 Type III  1.3 Biochip Products Segment by Application  1.3.1 Biochip Products Consumption Market Share by Application in 2015  1.3.2 Application 1  1.3.3 Application 2  1.3.4 Application 3  1.4 Biochip Products Market by Region  1.4.1 North America Status and Prospect (2011-2021)  1.4.2 Europe Status and Prospect (2011-2021)  1.4.3 China Status and Prospect (2011-2021)  1.4.4 Japan Status and Prospect (2011-2021)  1.4.5 Korea Status and Prospect (2011-2021)  1.4.6 Taiwan Status and Prospect (2011-2021)  1.5 Global Market Size (Value) of Biochip Products (2011-2021) 2 Global Biochip Products Market Competition by Manufacturers  2.1 Global Biochip Products Production and Share by Manufacturers (2015 and 2016)  2.2 Global Biochip Products Revenue and Share by Manufacturers (2015 and 2016)  2.3 Global Biochip Products Average Price by Manufacturers (2015 and 2016)  2.4 Manufacturers Biochip Products Manufacturing Base Distribution, Sales Area and Product Type  2.5 Biochip Products Market Competitive Situation and Trends  2.5.1 Biochip Products Market Concentration Rate  2.5.2 Biochip Products Market Share of Top 3 and Top 5 Manufacturers  2.5.3 Mergers & Acquisitions, Expansion 3 Global Biochip Products Production, Revenue (Value) by Region (2011-2016)  3.1 Global Biochip Products Production by Region (2011-2016)  3.2 Global Biochip Products Production Market Share by Region (2011-2016)  3.3 Global Biochip Products Revenue (Value) and Market Share by Region (2011-2016)  3.4 Global Biochip Products Production, Revenue, Price and Gross Margin (2011-2016)  3.5 North America Biochip Products Production, Revenue, Price and Gross Margin (2011-2016)  3.6 Europe Biochip Products Production, Revenue, Price and Gross Margin (2011-2016)  3.7 China Biochip Products Production, Revenue, Price and Gross Margin (2011-2016)  3.8 Japan Biochip Products Production, Revenue, Price and Gross Margin (2011-2016)  3.9 Korea Biochip Products Production, Revenue, Price and Gross Margin (2011-2016)  3.10 Taiwan Biochip Products Production, Revenue, Price and Gross Margin (2011-2016) For more information or any query mail at [email protected]


Patent
Hoffmann-La Roche and Dynamic Biosensors GmbH | Date: 2015-02-03

The present invention relates to a method of identifying a nucleotide at a defined position and determining the sequence of a target polynucleotide using an electro-switchable biosensor, as well as devices comprising an electro-switchable biosensor and uses thereof.

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