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HoogsCG

Development of a multiscale modeling strategy to decipher how hybrid DNA/RNA triplexes and G-quadruplexes affect gene expression regulation

Total Cost €

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EC-Contrib. €

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Partnership

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Project "HoogsCG" data sheet

The following table provides information about the project.

Coordinator
THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE 

Organization address
address: TRINITY LANE THE OLD SCHOOLS
city: CAMBRIDGE
postcode: CB2 1TN
website: www.cam.ac.uk

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 United Kingdom [UK]
 Project website http://mmb.pcb.ub.es/
 Total cost 195˙454 €
 EC max contribution 195˙454 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2014
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2015
 Duration (year-month-day) from 2015-05-01   to  2017-04-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE UK (CAMBRIDGE) coordinator 195˙454.00

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 Project objective

This proposal concerns the study of non-canonical interactions in nucleic acids. These interactions, also known as non-Watson-Crick base pairing, involve single or multiple DNA or RNA strands and are increasingly recognized as having a variety of essential roles in replication forks, telomeres, and gene regulation. Since these processes occur on spatial and time scales beyond the reach of current computational capabilities, we propose to develop an innovative coarse-grain approach to describe them. This approach will tackle an important and yet unmet challenge - the correct description of non-canonical interactions at near-atomic resolution in large-scale nucleic acids. The model will be derived from exhaustive classical all-atom molecular dynamics simulations and will be validated against experimental observables including nuclear magnetic resonance spectroscopy and small angle x-ray scattering. It will be used to describe non-canonical interactions – including Hoogsteen base pairs, which are the building blocks of triplex and quadruplex structures – and will incorporate the effects of epigenetic marks on DNA. The model will enable the description of the sequence dependent mechanical properties of guanine quadruplexes and triplex folds on temporal and spatial scales beyond the reach of current methods. As such, it will allow us to investigate the formation and dynamics of long triplex hybrids of DNA and RNA, the behaviour of long-non-coding RNAs interacting with naked DNA, and the effects of non-canonical interactions in systems relevant to chromatin. Thus, this model will be useful to predict and understand the molecular bases of fundamental open questions in biology and has a potential impact in molecular medicine and the pharmacological industry. Overall, this approach will provide an invaluable theoretical tool to describe nucleic acid structures and dynamics, contributing to the description and prediction of a wide range of genetic and epigenetic processes.

 Publications

year authors and title journal last update
List of publications.
2017 Julianne Kitevski-LeBlanc, Amélie Fradet-Turcotte, Predrag Kukic, Marcus D Wilson, Guillem Portella, Tairan Yuwen, Stephanie Panier, Shili Duan, Marella D Canny, Hugo van Ingen, Cheryl H Arrowsmith, John L Rubinstein, Michele Vendruscolo, Daniel Durocher, Lewis E Kay
The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage
published pages: , ISSN: 2050-084X, DOI: 10.7554/eLife.23872
eLife 6 2019-07-23
2015 Rosana Collepardo-Guevara, Guillem Portella, Michele Vendruscolo, Daan Frenkel, Tamar Schlick, Modesto Orozco
Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study
published pages: 10205-10215, ISSN: 0002-7863, DOI: 10.1021/jacs.5b04086
Journal of the American Chemical Society 137/32 2019-07-23
2017 Pablo D. Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco
How accurate are accurate force-fields for B-DNA?
published pages: gkw1355, ISSN: 0305-1048, DOI: 10.1093/nar/gkw1355
Nucleic Acids Research 2019-07-23
2015 Ivan Ivani, Pablo D Dans, Agnes Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluis Gelpí, Carlos González, Michele Vendruscolo, Charles A Laughton, Sarah A Harris, David A Case, Modesto Orozco
Parmbsc1: a refined force field for DNA simulations
published pages: , ISSN: 1548-7091, DOI: 10.1038/nmeth.3658
Nature Methods 2019-07-23

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