HoogsCG
Development of a multiscale modeling strategy to decipher how hybrid DNA/RNA triplexes and G-quadruplexes affect gene expression regulation
Total Cost €
0EC-Contrib. €
0Partnership
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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 contact info |
| 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.
| # | ||||
|---|---|---|---|---|
| 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 |
|---|---|---|---|
| 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 GelpÃ, 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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