Skip Navigation

Nucleic Acids Research 2005 33(9):2901-2907; doi:10.1093/nar/gki553
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (282K) Freely available
Right arrow Screen PDF (156K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (130)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Todd, A. K.
Right arrow Articles by Neidle, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Todd, A. K.
Right arrow Articles by Neidle, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 24 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Highly prevalent putative quadruplex sequence motifs in human DNA

Alan K. Todd, Matthew Johnston and Stephen Neidle*

CRUK Biomolecular Structure Group, The School of Pharmacy, University of London 29–39 Brunswick Square, London WC1N 1AX, UK

*To whom correspondence should be addressed. Tel: +44 020 7753 5969; Fax: +44 020 7753 5970; Email: stephen.neidle{at}ulsop.ac.uk

Received February 8, 2005. Revised March 29, 2005. Accepted April 16, 2005.

We report here the results of a systematic search for the existence and prevalence of potential intramolecular G-quadruplex forming sequences in the human genome. We have also examined the tendency for particular sequences of ‘loop’ regions to occur in particular positions with respect to the G-tracts in a quadruplex. Using arithmetic ratio and probability techniques we have discovered frequent and systematic occurrence of certain sequence types, the most prominent being a potential quadruplex containing CCTGT in the first ‘loop’ position. Being able to highlight types of potential quadruplex sequences in G-rich regions is an important step in searching for biologically relevant sequences and finding their function.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
K. Halder, M. Wieland, and J. S. Hartig
Predictable suppression of gene expression by 5'-UTR-based RNA quadruplexes
Nucleic Acids Res., November 1, 2009; 37(20): 6811 - 6817.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Du, Y. Zhao, and N. Li
Genome-wide colonization of gene regulatory elements by G4 DNA motifs
Nucleic Acids Res., November 1, 2009; 37(20): 6784 - 6798.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. I. Onyshchenko, T. I. Gaynutdinov, E. A. Englund, D. H. Appella, R. D. Neumann, and I. G. Panyutin
Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs
Nucleic Acids Res., October 9, 2009; (2009) gkp840v1.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
D. Drygin, A. Siddiqui-Jain, S. O'Brien, M. Schwaebe, A. Lin, J. Bliesath, C. B. Ho, C. Proffitt, K. Trent, J. P. Whitten, et al.
Anticancer Activity of CX-3543: A Direct Inhibitor of rRNA Biogenesis
Cancer Res., October 1, 2009; 69(19): 7653 - 7661.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
J. C. Darnell, C. E. Fraser, O. Mostovetsky, and R. B. Darnell
Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs
Hum. Mol. Genet., September 1, 2009; 18(17): 3164 - 3177.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Guedin, P. Alberti, and J.-L. Mergny
Stability of intramolecular quadruplexes: sequence effects in the central loop
Nucleic Acids Res., September 1, 2009; 37(16): 5559 - 5567.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nakken, T. Rognes, and E. Hovig
The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts
Nucleic Acids Res., September 1, 2009; 37(17): 5749 - 5756.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Verma, V. K. Yadav, R. Basundra, A. Kumar, and S. Chowdhury
Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells
Nucleic Acids Res., July 13, 2009; (2009) gkn1076v2.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
J. J. Wenzel, H. Rossmann, C. Fottner, S. Neuwirth, C. Neukirch, P. Lohse, J. K. Bickmann, T. Minnemann, T. J. Musholt, B. Schneider-Ratzke, et al.
Identification and Prevention of Genotyping Errors Caused by G-Quadruplex- and i-Motif-Like Sequences
Clin. Chem., July 1, 2009; 55(7): 1361 - 1371.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
O. Stegle, L. Payet, J.-L. Mergny, D. J. C. MacKay, and J. L. Huppert
Predicting and understanding the stability of G-quadruplexes
Bioinformatics, June 15, 2009; 25(12): i374 - i1382.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kumar, R. Basundra, and S. Maiti
Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
Nucleic Acids Res., June 1, 2009; 37(10): 3321 - 3331.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Kypr, I. Kejnovska, D. Renciuk, and M. Vorlickova
Circular dichroism and conformational polymorphism of DNA
Nucleic Acids Res., April 1, 2009; 37(6): 1713 - 1725.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Amrane, R. W. L. Ang, Z. M. Tan, C. Li, J. K. C. Lim, J. M. W. Lim, K. W. Lim, and A. T. Phan
A novel chair-type G-quadruplex formed by a Bombyx mori telomeric sequence
Nucleic Acids Res., February 1, 2009; 37(3): 931 - 938.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
S. D. Creacy, E. D. Routh, F. Iwamoto, Y. Nagamine, S. A. Akman, and J. P. Vaughn
G4 Resolvase 1 Binds Both DNA and RNA Tetramolecular Quadruplex with High Affinity and Is the Major Source of Tetramolecular Quadruplex G4-DNA and G4-RNA Resolving Activity in HeLa Cell Lysates
J. Biol. Chem., December 12, 2008; 283(50): 34626 - 34634.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. L. Huppert, A. Bugaut, S. Kumari, and S. Balasubramanian
G-quadruplexes: the beginning and end of UTRs
Nucleic Acids Res., November 1, 2008; 36(19): 6260 - 6268.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kumar and S. Maiti
A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes
Nucleic Acids Res., October 1, 2008; 36(17): 5610 - 5622.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kumar, B. Sahoo, K. A. S. Varun, S. Maiti, and S. Maiti
Effect of loop length variation on quadruplex-Watson Crick duplex competition
Nucleic Acids Res., August 1, 2008; 36(13): 4433 - 4442.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
A. Arora, M. Dutkiewicz, V. Scaria, M. Hariharan, S. Maiti, and J. Kurreck
Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif
RNA, July 1, 2008; 14(7): 1290 - 1296.
[Abstract] [Full Text] [PDF]

Home page
 Mol Cancer ResHome page
F.-C. Huang, C.-C. Chang, P.-J. Lou, I-C. Kuo, C.-W. Chien, C.-T. Chen, F.-Y. Shieh, T.-C. Chang, and J.-J. Lin
G-Quadruplex Stabilizer 3,6-Bis(1-Methyl-4-Vinylpyridinium)Carbazole Diiodide Induces Accelerated Senescence and Inhibits Tumorigenic Properties in Cancer Cells
Mol. Cancer Res., June 1, 2008; 6(6): 955 - 964.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. K. Todd and S. Neidle
The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements
Nucleic Acids Res., May 1, 2008; 36(8): 2700 - 2704.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Eddy and N. Maizels
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes
Nucleic Acids Res., March 27, 2008; 36(4): 1321 - 1333.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
Z. Du, Y. Zhao, and N. Li
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription
Genome Res., February 1, 2008; 18(2): 233 - 241.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. G. Hershman, Q. Chen, J. Y. Lee, M. L. Kozak, P. Yue, L.-S. Wang, and F. B. Johnson
Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae
Nucleic Acids Res., January 17, 2008; 36(1): 144 - 156.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Zhang, Y. Lin, and C.-T. Zhang
Greglist: a database listing potential G-quadruplex regulated genes
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D372 - D376.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. K. Yadav, J. K. Abraham, P. Mani, R. Kulshrestha, and S. Chowdhury
QuadBase: genome-wide database of G4 DNA occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D381 - D385.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. Kikin, Z. Zappala, L. D'Antonio, and P. S. Bagga
GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D141 - D148.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc AHome page
J. L. Huppert
Four-stranded DNA: cancer, gene regulation and drug development
Phil Trans R Soc A, December 15, 2007; 365(1861): 2969 - 2984.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. J. Patel, A. T. Phan, and V. Kuryavyi
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics
Nucleic Acids Res., December 3, 2007; 35(22): 7429 - 7455.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. K. Todd, S. M. Haider, G. N. Parkinson, and S. Neidle
Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter
Nucleic Acids Res., September 27, 2007; 35(17): 5799 - 5808.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Pharmacol.Home page
B. Brassart, D. Gomez, A. D. Cian, R. Paterski, A. Montagnac, K.-H. Qui, N. Temime-Smaali, C. Trentesaux, J.-L. Mergny, F. Gueritte, et al.
A New Steroid Derivative Stabilizes G-Quadruplexes and Induces Telomere Uncapping in Human Tumor Cells
Mol. Pharmacol., September 1, 2007; 72(3): 631 - 640.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. A. Rachwal, I. S. Findlow, J. M. Werner, T. Brown, and K. R. Fox
Intramolecular DNA quadruplexes with different arrangements of short and long loops
Nucleic Acids Res., June 18, 2007; (2007) gkm316v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Yao, Q. Wang, Y.-h. Hao, and Z. Tan
An exonuclease I hydrolysis assay for evaluating G-quadruplex stabilization by small molecules
Nucleic Acids Res., May 14, 2007; 35(9): e68 - e68.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. L. Huppert and S. Balasubramanian
G-quadruplexes in promoters throughout the human genome
Nucleic Acids Res., January 28, 2007; 35(2): 406 - 413.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
D. Gomez, T. Wenner, B. Brassart, C. Douarre, M.-F. O'Donohue, V. El Khoury, K. Shin-ya, H. Morjani, C. Trentesaux, and J.-F. Riou
Telomestatin-induced Telomere Uncapping Is Modulated by POT1 through G-overhang Extension in HT1080 Human Tumor Cells
J. Biol. Chem., December 15, 2006; 281(50): 38721 - 38729.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Burge, G. N. Parkinson, P. Hazel, A. K. Todd, and S. Neidle
Quadruplex DNA: sequence, topology and structure
Nucleic Acids Res., November 14, 2006; 34(19): 5402 - 5415.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Eddy and N. Maizels
Gene function correlates with potential for G4 DNA formation in the human genome
Nucleic Acids Res., September 1, 2006; 34(14): 3887 - 3896.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. Kikin, L. D'Antonio, and P. S Bagga
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W676 - W682.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Scaria, M. Hariharan, A. Arora, and S. Maiti
Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W683 - W685.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. L. Youds, N. J. O'Neil, and A. M. Rose
Homologous Recombination Is Required for Genome Stability in the Absence of DOG-1 in Caenorhabditis elegans
Genetics, June 1, 2006; 173(2): 697 - 708.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
P. Rawal, V. B. R. Kummarasetti, J. Ravindran, N. Kumar, K. Halder, R. Sharma, M. Mukerji, S. K. Das, and S. Chowdhury
Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation.
Genome Res., May 1, 2006; 16(5): 644 - 655.
[Abstract] [Full Text] [PDF]

Home page
 J. Immunol.Home page
J. Kralovicova and I. Vorechovsky
Position-Dependent Repression and Promotion of DQB1 Intron 3 Splicing by GGGG Motifs
J. Immunol., February 15, 2006; 176(4): 2381 - 2388.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Xu and H. Sugiyama
Formation of the G-quadruplex and i-motif structures in retinoblastoma susceptibility genes (Rb)
Nucleic Acids Res., February 7, 2006; 34(3): 949 - 954.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Hazel, G. N Parkinson, and S. Neidle
Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.
Nucleic Acids Res., January 1, 2006; 34(7): 2117 - 2127.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Kostadinov, N. Malhotra, M. Viotti, R. Shine, L. D'Antonio, and P. Bagga
GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D119 - D124.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kumar and S. Maiti
The effect of osmolytes and small molecule on Quadruplex-WC duplex equilibrium: a fluorescence resonance energy transfer study
Nucleic Acids Res., November 30, 2005; 33(21): 6723 - 6732.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Li, J. J. Correia, L. Wang, J. O. Trent, and J. B. Chaires
Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal
Nucleic Acids Res., August 16, 2005; 33(14): 4649 - 4659.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. L. Huppert and S. Balasubramanian
Prevalence of quadruplexes in the human genome
Nucleic Acids Res., May 24, 2005; 33(9): 2908 - 2916.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.