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ZIPgeting SIGNED

Quantitative understanding of target recognition on DNA based on directional zipping processes

Total Cost €

EC-Contrib. €

Partnership

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ZIPgeting project word cloud

Explore the words cloud of the ZIPgeting project. It provides you a very rough idea of what is the project "ZIPgeting" about.

programmability live promoted recognize molecule identification protein edge refined obtain combined equilibrium dna parallelized decipher revealed sequences predictors degradation cutting flexible coupled detection synthetic mechanism enzymes cas throughput mechanisms directional tested zipping base predictions unifying engineering tens models crispr specificity mechanistic off pairs binding mechanical data understand first recognition twisting regulation cells environment imaging single enormous physics allosteric biology tales proteins genome parallel programmable experiments fluorescence quantitative characterization manner employed sequence goals precise

Project "ZIPgeting" data sheet

The following table provides information about the project.

Coordinator	UNIVERSITAET LEIPZIG Organization address address: RITTERSTRASSE 26 city: LEIPZIG postcode: 4109 website: www.uni-Ieipzig.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Germany [DE]
Total cost	2˙000˙000 €
EC max contribution	2˙000˙000 € (100%)
Programme	1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
Code Call	ERC-2016-COG
Funding Scheme	ERC-COG
Starting year	2017
Duration (year-month-day)	from 2017-05-01 to 2022-04-30

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	UNIVERSITAET LEIPZIG UNIVERSITAET LEIPZIG Organization address address: RITTERSTRASSE 26 city: LEIPZIG postcode: 4109 website: www.uni-Ieipzig.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (LEIPZIG)	coordinator	2˙000˙000.00

Map

Project objective

In the recent years a number of protein systems have been identified that recognize long (tens of base pairs) DNA sequences and allow flexible programmability of their target specificity. This promoted an enormous range of applications in genome engineering and synthetic biology. This project aims to decipher the mechanisms by which these proteins recognize their DNA targets in order to develop quantitative models/predictors for target recognition and to avoid off-target effects. To obtain detailed insight into the targeting mechanisms of different programmable systems in a “bottom-up manner”, cutting-edge single-molecule experiments, such as mechanical DNA twisting combined with single-molecule fluorescence detection will be employed. This will provide a fully quantitative characterization of the targeting process and insight into the mechanisms of allosteric regulation coupled to targeting. The quantitative data will allow to develop physics-based models of the target recognition process. In particular, we will focus on recognition through non-equilibrium, directional zipping along the target sequence – as recently revealed for CRISPR-Cas enzymes – as a promising unifying mechanism. To obtain precise targeting predictors our first-principle models will be tested and refined using high-throughput measurements on many different targets in parallel. Finally, the predictions will be used in order to understand target selection in live cells using single-molecule imaging. Within the project the following goals are defined: Goal 1: Quantitative understanding of target binding/degradation for CRISPR-Cas systems Goal 2: Detailed mechanistic insight into the target recognition process by TALEs Goal 3: Development of highly parallelized measurements on different target sequences down to the single-molecule level Goal 4: Target identification in the complex environment of live cells

Publications

List of publications.
year	authors and title	journal	last update
2019	Inga Songailiene, Marius Rutkauskas, Tomas Sinkunas, Elena Manakova, Sabine Wittig, Carla Schmidt, Virginijus Siksnys, Ralf Seidel Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length published pages: 3157-3166.e4, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2019.08.033	Cell Reports 28/12	2020-01-14
2019	Kristina Kasaciunaite, Fergus Fettes, Maryna Levikova, Peter Daldrop, Roopesh Anand, Petr Cejka, Ralf Seidel Competing interaction partners modulate the activity of Sgs1 helicase during DNA end resection published pages: , ISSN: 0261-4189, DOI: 10.15252/embj.2019101516	The EMBO Journal 38/13	2020-01-14
2018	Andrey Krivoy, Marius Rutkauskas, Konstantin Kuznedelov, Olga Musharova, Christophe Rouillon, Konstantin Severinov, Ralf Seidel Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro published pages: 4087-4098, ISSN: 0305-1048, DOI: 10.1093/nar/gky219	Nucleic Acids Research 46/8	2019-04-18

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