Nucleic Acids Research Advance Access originally published online on August 30, 2008
Nucleic Acids Research 2008 36(17):5610-5622; doi:10.1093/nar/gkn543
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, No. 17 5610-5622
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes
Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
*To whom correspondence should be addressed. Tel: +91 11 2766 6156; Fax: +91 11 2766 7471; Email: souvik{at}igib.res.in
Received February 29, 2008. Revised August 7, 2008. Accepted August 8, 2008.
Loop length and its composition are important for the structural and functional versatility of quadruplexes. To date studies on the loops have mainly concerned model sequences compared with naturally occurring quadruplex sequences which have diverse loop lengths and compositions. Herein, we have characterized 36 quadruplex-forming sequences from the promoter regions of various proto-oncogenes using CD, UV and native gel electrophoresis. We examined folding topologies and determined the thermodynamic profile for quadruplexes varying in total loop length (5–18 bases) and composition. We found that naturally occurring quadruplexes have variable thermodynamic stabilities (
G37) ranging from –1.7 to –15.6 kcal/mol. Overall, our results suggest that both loop length and its composition affect quadruplex structure and thermodynamics, thus making it difficult to draw generalized correlations between loop length and thermodynamic stability. Additionally, we compared the thermodynamic stability of quadruplexes and their respective duplexes to understand quadruplex–duplex competition. Our findings invoke a discussion on whether biological function is associated with quadruplexes with lower thermodynamic stability which undergo facile formation and disruption, or by quadruplexes with high thermodynamic stability.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|