Cargando…

G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool

We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro forma...

Descripción completa

Detalles Bibliográficos
Autores principales: Belmonte-Reche, Efres, Morales, Juan Carlos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671307/
https://www.ncbi.nlm.nih.gov/pubmed/33575559
http://dx.doi.org/10.1093/nargab/lqz005
_version_ 1783610905234243584
author Belmonte-Reche, Efres
Morales, Juan Carlos
author_facet Belmonte-Reche, Efres
Morales, Juan Carlos
author_sort Belmonte-Reche, Efres
collection PubMed
description We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro formation probability and presence of known-to-form structures are then used as filters. The outcome is an efficient methodology that helps select the best candidates for a subsequent in vitro analysis or a macroscopic genomic quadruplex assessment. As proof of the analytical capabilities of G4-iM Grinder, the human genome was analyzed for potential G4s and i-Motifs. Many known-to-form structures were identified. New candidates were selected considering their score and appearance frequency. We also focused on locating Potential Higher Order Quadruplex Sequences (PHOQS). We developed a new methodology to predict the most probable subunits of these assemblies and applied it to a PHOQS candidate. Taking the human average density as reference, we examined the genomes of several etiological causes of disease. This first of its class comparative study found many organisms to be very dense in these potential quadruplexes. Many presented already known-to-form-G4s and i-Motifs. These findings suggest the potential quadruplexes have as therapeutic targets for these diseases that currently kill millions worldwide.
format Online
Article
Text
id pubmed-7671307
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-76713072021-02-10 G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool Belmonte-Reche, Efres Morales, Juan Carlos NAR Genom Bioinform Standard Article We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro formation probability and presence of known-to-form structures are then used as filters. The outcome is an efficient methodology that helps select the best candidates for a subsequent in vitro analysis or a macroscopic genomic quadruplex assessment. As proof of the analytical capabilities of G4-iM Grinder, the human genome was analyzed for potential G4s and i-Motifs. Many known-to-form structures were identified. New candidates were selected considering their score and appearance frequency. We also focused on locating Potential Higher Order Quadruplex Sequences (PHOQS). We developed a new methodology to predict the most probable subunits of these assemblies and applied it to a PHOQS candidate. Taking the human average density as reference, we examined the genomes of several etiological causes of disease. This first of its class comparative study found many organisms to be very dense in these potential quadruplexes. Many presented already known-to-form-G4s and i-Motifs. These findings suggest the potential quadruplexes have as therapeutic targets for these diseases that currently kill millions worldwide. Oxford University Press 2019-09-30 /pmc/articles/PMC7671307/ /pubmed/33575559 http://dx.doi.org/10.1093/nargab/lqz005 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Standard Article
Belmonte-Reche, Efres
Morales, Juan Carlos
G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
title G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
title_full G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
title_fullStr G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
title_full_unstemmed G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
title_short G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
title_sort g4-im grinder: when size and frequency matter. g-quadruplex, i-motif and higher order structure search and analysis tool
topic Standard Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671307/
https://www.ncbi.nlm.nih.gov/pubmed/33575559
http://dx.doi.org/10.1093/nargab/lqz005
work_keys_str_mv AT belmonterecheefres g4imgrinderwhensizeandfrequencymattergquadrupleximotifandhigherorderstructuresearchandanalysistool
AT moralesjuancarlos g4imgrinderwhensizeandfrequencymattergquadrupleximotifandhigherorderstructuresearchandanalysistool