Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ).
Bulge
Classification of G-quadruplexes
G-Tetrad
G-quadruplex
Loop
Secondary structures
Journal
Journal of computer-aided molecular design
ISSN: 1573-4951
Titre abrégé: J Comput Aided Mol Des
Pays: Netherlands
ID NLM: 8710425
Informations de publication
Date de publication:
29 Oct 2024
29 Oct 2024
Historique:
received:
10
06
2024
accepted:
30
08
2024
medline:
29
10
2024
pubmed:
29
10
2024
entrez:
29
10
2024
Statut:
epublish
Résumé
G-quadruplexes refer to a large group of nucleic acid-based structures. In recent years, they have been attracting attention due to their biological roles in the telomeres and promoter regions. These structures show wide diversity in topology, however, development of methods for structural classification of G-quadruplexes has been evaded for a long time. There has been a limited number of studies aiming to bring forth a secondary structure classification method. The situation was even more complex than imagined, since the discovery of bulged and mismatched G-quadruplexes while most of the available tools fail to distinguish these non-canonical G-quadruplex motifs. Moreover, the interpretation of their analysis output still requires expert knowledge. In this study, we propose a new method for identification of unimolecular G-Quadruplexes and classification by secondary structures based on three-dimensional structural data. Briefly, coordinates of guanines are processed to identify tetrads, loops and bulges. Then, we present the secondary structure in the form of a depiction which shows the loop types, bulges, and guanines that participate in each tetrad. Moreover, CIIS-GQ identifies non-guanine nucleotides that joins the G-tetrads and forms multiplets. Finally, the results of our study are compared with DSSR and ElTetrado classification methods, and the advantages of the proposed depiction method for representing secondary structures were discussed. The source code of the method can be accessed via https://github.com/TugayDirek/CIIS-GQ .
Identifiants
pubmed: 39470927
doi: 10.1007/s10822-024-00573-1
pii: 10.1007/s10822-024-00573-1
doi:
Substances chimiques
Guanine
5Z93L87A1R
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
35Subventions
Organisme : Türkiye Bilimsel ve Teknolojik Araştırma Kurumu
ID : 216S854
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
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