Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (292K) Freely available
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 (65)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Risitano, A.
Right arrow Articles by Fox, K. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Risitano, A.
Right arrow Articles by Fox, K. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 11 May 2004

Nucleic Acids Research, 2004, Vol. 32, No. 8 2598-2606
© 2004 Oxford University Press

Influence of loop size on the stability of intramolecular DNA quadruplexes

Antonina Risitano and Keith R. Fox*

School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK

*To whom correspondence should be addressed. Tel: +44 23 8059 4374; Fax: +44 23 8059 4459; Email: K.R.Fox{at}soton.ac.uk
Present address: Antonina Risitano, School of Medicine, New York University, 550 First Avenue, New York, NY 10016, USA

Received February 11, 2004; Revised and Accepted April 19, 2004

We have determined the stability of intramolecular DNA quadruplexes in which the four G3-tracts are connected by non-nucleosidic linkers containing propanediol, octanediol or hexaethylene glycol, replacing the TTA loops in the human telomeric repeat sequence. We find that these sequences all fold to form intramolecular complexes, which are stabilized by lithium < sodium < potassium. Quadruplex stability increases in the order propanediol < hexaethylene glycol < octanediol. The shallower shape of the melting profile with propanediol linkers and its lower dependency on potassium concentration suggests that this complex contains fewer stacks of G-quartets. The sequence with octanediol linkers displays a biphasic melting profile, suggesting that it can adopt more than one stable structure. All these complexes display melting temperatures above 310 K in the presence of 10 mM lithium, without added potassium, in contrast to the telomeric repeat sequence. These complexes also fold much faster than the telomeric repeat and there is little or no hysteresis between their melting and annealing profiles. In contrast, the human telomeric repeat sequence and a complex containing two hexaethylene glycol groups in each loop, are less stable and fold more slowly. The melting and annealing profiles for the latter sequence show significant differences, even when heated at 0.2°C min–1. CD spectra for the oligonucleotides containing non-nucleosidic linkers show positive maxima at 264 nm, with negative minima ~244 nm, which are characteristic of parallel quadruplex structures. These results show that the structure and stability of intramolecular quadruplexes is profoundly influenced by the length and composition of the loops.


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
A. Guedin, P. Alberti, and J.-L. Mergny
Stability of intramolecular quadruplexes: sequence effects in the central loop
Nucleic Acids Res., July 6, 2009; (2009) gkp563v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Michalowski, R. Chitima-Matsiga, D. M. Held, and D. H. Burke
Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases
Nucleic Acids Res., December 1, 2008; 36(22): 7124 - 7135.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. N. Lane, J. B. Chaires, R. D. Gray, and J. O. Trent
Stability and kinetics of G-quadruplex structures
Nucleic Acids Res., October 1, 2008; 36(17): 5482 - 5515.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Guo, V. Gokhale, L. H. Hurley, and D. Sun
Intramolecularly folded G-quadruplex and i-motif structures in the proximal promoter of the vascular endothelial growth factor gene
Nucleic Acids Res., August 1, 2008; 36(14): 4598 - 4608.
[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
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
Y. Qin, E. M. Rezler, V. Gokhale, D. Sun, and L. H. Hurley
Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4
Nucleic Acids Res., December 3, 2007; 35(22): 7698 - 7713.
[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
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
 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
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
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
A. K. Todd, M. Johnston, and S. Neidle
Highly prevalent putative quadruplex sequence motifs in human DNA
Nucleic Acids Res., May 24, 2005; 33(9): 2901 - 2907.
[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.