G4Bank: A database of experimentally identified DNA G-quadruplex sequences

被引:6
|
作者
Zhong, Hong-Sheng [1 ]
Dong, Mei-Jing [1 ]
Gao, Feng [1 ,2 ,3 ,4 ]
机构
[1] Tianjin Univ, Sch Sci, Dept Phys, Tianjin 300072, Peoples R China
[2] Tianjin Univ, Frontiers Sci Ctr Synthet Biol, Tianjin 300072, Peoples R China
[3] Tianjin Univ, Key Lab Syst Bioengn, Minist Educ, Tianjin 300072, Peoples R China
[4] Collaborat Innovat Ctr Chem Sci & Engn Tianjin, SynBio Res Platform, Tianjin 300072, Peoples R China
基金
中国国家自然科学基金;
关键词
DNA G-quadruplex; Database; Sequence analysis; Genome-wide; REPLICATION; STABILITY;
D O I
10.1007/s12539-023-00577-9
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
G-quadruplex (G4), a non-canonical nucleic acid structure, has been suggested to play a key role in important cellular processes including transcription, replication and cancer development. Recently, high-throughput sequencing approaches for G4 detection have provided a large amount of experimentally identified G4 data that reveal genome-wide G4 landscapes and enable the development of new methods for predicting potential G4s from sequences. Although several existing databases provide G4 experimental data and relevant biological information from different perspectives, there is no dedicated database to collect and analyze DNA G4 experimental data genome-widely. Here, we constructed G4Bank, a database of experimentally identified DNA G-quadruplex sequences. A total of 6,915,983 DNA G4s were collected from 13 organisms, and state-of-the-art prediction methods were performed to filter and analyze the G4 data. Therefore, G4Bank will facilitate users to access comprehensive G4 experimental data and enable sequence feature analysis of G4 for further investigation. The database of the experimentally identified DNA G-quadruplex sequences can be accessed at http://tubic.tju.edu.cn/g4bank/. [GRAPHICS] .
引用
收藏
页码:515 / 523
页数:9
相关论文
共 50 条
  • [21] Simultaneous G-Quadruplex DNA Logic
    Bader, Antoine
    Cockroft, Scott L.
    CHEMISTRY-A EUROPEAN JOURNAL, 2018, 24 (19) : 4820 - 4824
  • [22] New G-quadruplex DNA structures
    Shivachev, Boris L.
    Dimowa, Louiza T.
    Nikolova, Rosica P.
    Sbirkova, Hristina I.
    Tzvetanova, Lilia
    Hristoff, Peter
    Radoslavov, Georgi
    Tzanko, Doukov I.
    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2015, 71 : S247 - S247
  • [23] G-quadruplex targeting chemical nucleases as a nonperturbative tool for analysis of cellular G-quadruplex DNA
    Yu, Zhen
    Hendricks, Amber L.
    Cowan, James A.
    ISCIENCE, 2021, 24 (06)
  • [24] Click Chemistry for the Identification of G-Quadruplex Structures: Discovery of a DNA-RNA G-Quadruplex
    Xu, Yan
    Suzuki, Yuta
    Komiyama, Makoto
    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2009, 48 (18) : 3281 - 3284
  • [25] Evidences for Piperine inhibiting cancer by targeting human G-quadruplex DNA sequences
    Tawani, Arpita
    Amanullah, Ayeman
    Mishra, Amit
    Kumar, Amit
    SCIENTIFIC REPORTS, 2016, 6
  • [26] Evidences for Piperine inhibiting cancer by targeting human G-quadruplex DNA sequences
    Arpita Tawani
    Ayeman Amanullah
    Amit Mishra
    Amit Kumar
    Scientific Reports, 6
  • [27] Using Macrocyclic G-Quadruplex Ligands to Decipher the Interactions Between Small Molecules and G-Quadruplex DNA
    Andreasson, Mans
    Bhuma, Naresh
    Pemberton, Nils
    Chorell, Erik
    CHEMISTRY-A EUROPEAN JOURNAL, 2022, 28 (65)
  • [28] G-Quadruplex Sequences are Barriers to Replicative DNA Polymerases and Hotspots of Mutagenesis.
    Eckert, K. A.
    Hile, S. E.
    Guiblet, W.
    Cremona, M.
    Stein, M. E.
    Huang, Y. F.
    Chiaromonte, F.
    Makova, K. D.
    ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, 2020, 61 : 47 - 47
  • [29] Replication Control of Human Telomere G-Quadruplex DNA by G-Quadruplex Ligands Dependent on Solution Environment
    Takahashi, Shuntaro
    Bhowmik, Sudipta
    Sato, Shinobu
    Takenaka, Shigeori
    Sugimoto, Naoki
    LIFE-BASEL, 2022, 12 (04):
  • [30] Monomorphic RNA G-Quadruplex and Polymorphic DNA G-Quadruplex Structures Responding to Cellular Environmental Factors
    Zhang, Dong-Hao
    Fujimoto, Takeshi
    Saxena, Sarika
    Yu, Hai-Qing
    Miyoshi, Daisuke
    Sugimoto, Naoki
    BIOCHEMISTRY, 2010, 49 (21) : 4554 - 4563