Skip Navigation

Nucleic Acids Research 2005 33(Web Server Issue):W577-W581; doi:10.1093/nar/gki591
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (95K) Freely available
Right arrow Screen PDF (100K) 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 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 Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Markham, N. R.
Right arrow Articles by Zuker, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Markham, N. R.
Right arrow Articles by Zuker, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

DINAMelt web server for nucleic acid melting prediction

Nicholas R. Markham1 and Michael Zuker2,*

1Department of Computer Science, Rensselaer Polytechnic Institute Troy, NY 12180-3590, USA 2Department of Mathematical Sciences, Rensselaer Polytechnic Institute Troy, NY 12180-3590, USA

*To whom correspondence should be addressed. Tel: +1 518 276 6902; Fax: +1 518 276 4824; Email: zukerm{at}rpi.edu

Received February 14, 2005. Revised April 18, 2005. Accepted May 5, 2005.

The DINAMelt web server simulates the melting of one or two single-stranded nucleic acids in solution. The goal is to predict not just a melting temperature for a hybridized pair of nucleic acids, but entire equilibrium melting profiles as a function of temperature. The two molecules are not required to be complementary, nor must the two strand concentrations be equal. Competition among different molecular species is automatically taken into account. Calculations consider not only the heterodimer, but also the two possible homodimers, as well as the folding of each single-stranded molecule. For each of these five molecular species, free energies are computed by summing Boltzmann factors over every possible hybridized or folded state. For temperatures within a user-specified range, calculations predict species mole fractions together with the free energy, enthalpy, entropy and heat capacity of the ensemble. Ultraviolet (UV) absorbance at 260 nm is simulated using published extinction coefficients and computed base pair probabilities. All results are available as text files and plots are provided for species concentrations, heat capacity and UV absorbance versus temperature. This server is connected to an active research program and should evolve as new theory and software are developed. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/.


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
G. P. Brewood, Y. Rangineni, D. J. Fish, A. S. Bhandiwad, D. R. Evans, R. Solanki, and A. S. Benight
Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes
Nucleic Acids Res., July 15, 2008; (2008) gkn436v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. D. Gans and M. Wolinsky
Improved assay-dependent searching of nucleic acid sequence databases
Nucleic Acids Res., July 1, 2008; 36(12): e74 - e74.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. H. T. Nelissen, A. J. van Gammeren, M. Tessari, F. C. Girard, H. A. Heus, and S. S. Wijmenga
Multiple segmental and selective isotope labeling of large RNA for NMR structural studies
Nucleic Acids Res., June 26, 2008; (2008) gkn397v1.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. M. Miller, D. M. Tourlousse, R. D. Stedtfeld, S. W. Baushke, A. B. Herzog, L. M. Wick, J. M. Rouillard, E. Gulari, J. M. Tiedje, and S. A. Hashsham
In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water
Appl. Envir. Microbiol., April 1, 2008; 74(7): 2200 - 2209.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Petersen, L. Poulsen, S. Petronis, H. Birgens, and M. Dufva
Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays
Nucleic Acids Res., February 2, 2008; 36(2): e10 - e10.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Y.-C. Lin, L.-C. Hsieh, M.-W. Kuo, J. Yu, H.-H. Kuo, W.-L. Lo, R.-J. Lin, A. L. Yu, and W.-H. Li
Human TRIM71 and Its Nematode Homologue Are Targets of let-7 MicroRNA and Its Zebrafish Orthologue Is Essential for Development
Mol. Biol. Evol., November 1, 2007; 24(11): 2525 - 2534.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. Schwartz, E. Margeat, A. R. Rahmouni, and M. Boudvillain
Transcription Termination Factor Rho Can Displace Streptavidin from Biotinylated RNA
J. Biol. Chem., October 26, 2007; 282(43): 31469 - 31476.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Buratti, M. Chivers, J. Kralovicova, M. Romano, M. Baralle, A. R. Krainer, and I. Vorechovsky
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization
Nucleic Acids Res., July 26, 2007; 35(13): 4250 - 4263.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
C. J. Paredes, R. S. Senger, I. S. Spath, J. R. Borden, R. Sillers, and E. T. Papoutsakis
A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum
Appl. Envir. Microbiol., July 15, 2007; 73(14): 4631 - 4638.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
E. Burkala, J. M. Reimers, K. H. Schmidt, N. Davis, P. Wei, and B. E. Wright
Secondary structures as predictors of mutation potential in the lacZ gene of Escherichia coli
Microbiology, July 1, 2007; 153(7): 2180 - 2189.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Feng and E. R.M. Tillier
A fast and flexible approach to oligonucleotide probe design for genomes and gene families
Bioinformatics, May 15, 2007; 23(10): 1195 - 1202.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
J.-M. Lanchy and J. S. Lodmell
An Extended Stem-Loop 1 Is Necessary for Human Immunodeficiency Virus Type 2 Replication and Affects Genomic RNA Encapsidation
J. Virol., April 1, 2007; 81(7): 3285 - 3292.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
B. Hobl and M. Mack
The regulator protein PyrR of Bacillus subtilis specifically interacts in vivo with three untranslated regions within pyr mRNA of pyrimidine biosynthesis
Microbiology, March 1, 2007; 153(3): 693 - 700.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Bishop, C. Wilson, A. M. Chagovetz, and S. Blair
Competitive Displacement of DNA during Surface Hybridization
Biophys. J., January 1, 2007; 92(1): L10 - L12.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Bishop, S. Blair, and A. M. Chagovetz
A Competitive Kinetic Model of Nucleic Acid Surface Hybridization in the Presence of Point Mutants
Biophys. J., February 1, 2006; 90(3): 831 - 840.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Tjaden, S. S. Goodwin, J. A. Opdyke, M. Guillier, D. X. Fu, S. Gottesman, and G. Storz
Target prediction for small, noncoding RNAs in bacteria.
Nucleic Acids Res., January 1, 2006; 34(9): 2791 - 2802.
[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.