Skip Navigation

Nucleic Acids Research 2004 32(20):6144-6151; doi:10.1093/nar/gkh954
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (359K) Freely available
Right arrow Supplementary Material
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 (24)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Pérez, A.
Right arrow Articles by Orozco, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pérez, A.
Right arrow Articles by Orozco, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 23 November 2004

Nucleic Acids Research, Vol. 32 No. 20 © Oxford University Press 2004; all rights reserved

The relative flexibility of B-DNA and A-RNA duplexes: database analysis

Alberto Pérez1, Agnes Noy1, Filip Lankas2, F. Javier Luque3 and Modesto Orozco1,4,*

1 Molecular Modelling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, 2 Institute for Mathematics B, EPFL (Swiss Federal Polytechnical Institute), 1015 Lausanne, Switzerland, 3 Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain and 4 Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain

* To whom correspondence should be addressed. Tel: +34 93 403 71 57; Fax: +34 93 403 71 56; Email: modesto{at}mmb.pcb.ub.es

Received July 8, 2004; Revised September 9, 2004; Accepted November 2, 2004

An extensive analysis of structural databases is carried out to investigate the relative flexibility of B-DNA and A-RNA duplexes in crystal form. Our results show that the general anisotropic concept of flexibility is not very useful to compare the deformability of B-DNA and A-RNA duplexes, since the flexibility patterns of B-DNA and A-RNA are quite different. In other words, ‘flexibility’ is a dangerous word for describing macromolecules, unless it is clearly defined. A few soft essential movements explain most of the natural flexibility of A-RNA, whereas many are necessary for B-DNA. Essential movements occurring in naked B-DNAs are identical to those necessary to deform DNA in DNA–protein complexes, which suggest that evolution has designed DNA–protein complexes so that B-DNA is deformed according to its natural tendency. DNA is generally more flexible, but for some distortions A-RNA is easier to deform. Local stiffness constants obtained for naked B-DNAs and DNA complexes are very close, demonstrating that global distortions in DNA necessary for binding to proteins are the result of the addition of small concerted deformations at the base-pair level. Finally, it is worth noting that in general the picture of the relative deformability of A-RNA and DNA derived from database analysis agrees very well with that derived from state of the art molecular dynamics (MD) simulations.


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
 Biophys. JHome page
S. Fulle and H. Gohlke
Analyzing the Flexibility of RNA Structures by Constraint Counting
Biophys. J., June 1, 2008; 94(11): 4202 - 4219.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Perez, F. Lankas, F. J. Luque, and M. Orozco
Towards a molecular dynamics consensus view of B-DNA flexibility
Nucleic Acids Res., April 1, 2008; 36(7): 2379 - 2394.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
C. Musselman, H. M. Al-Hashimi, and I. Andricioaei
iRED Analysis of TAR RNA Reveals Motional Coupling, Long-Range Correlations, and a Dynamical Hinge
Biophys. J., July 15, 2007; 93(2): 411 - 422.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. Perez, I. Marchan, D. Svozil, J. Sponer, T. E. Cheatham III, C. A. Laughton, and M. Orozco
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of {alpha}/{gamma} Conformers
Biophys. J., June 1, 2007; 92(11): 3817 - 3829.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Noy, A. Perez, C. A. Laughton, and M. Orozco
Theoretical study of large conformational transitions in DNA: the B{leftrightarrow}A conformational change in water and ethanol/water
Nucleic Acids Res., May 11, 2007; 35(10): 3330 - 3338.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Joli, N. Bouchemal, A. Laigle, B. Hartmann, and E. Hantz
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides
Nucleic Acids Res., November 6, 2006; 34(20): 5740 - 5751.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
E. Cubero, F. J. Luque, and M. Orozco
Theoretical Study of the Hoogsteen-Watson-Crick Junctions in DNA
Biophys. J., February 1, 2006; 90(3): 1000 - 1008.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nikolajewa, A. Beyer, M. Friedel, J. Hollunder, and T. Wilhelm
Common patterns in type II restriction enzyme binding sites
Nucleic Acids Res., May 11, 2005; 33(8): 2726 - 2733.
[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.