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Nick Markham, a graduate student in computer science,
created the DINAMelt web server that uses his comprehensive
package of nucleic acid hybridization and folding programs.
Michael Zuker,
professor of mathematical sciences, and biology,
develops tools for predicting hybridization and
folding (secondary structure) of DNA and RNA using
equilibrium thermodynamic methods. Much of his work
has been on RNA structure, which is important in
understanding many biological processes, including
translation regulation in messenger RNA, replication
of single-stranded RNA viruses, and the function of
structural RNAs and RNA/protein complexes. His
algorithms have been widely used for drug design, and
work on DNA folding has been very popular with the
biotechnology community. Recent work in his
laboratory includes the development of methods to
predict hybridization, folding and melting profiles
for two strands of DNA or RNA. This hybridization web
server offers newly devloped software to the
scientific community. The older "mfold" web server has
been very popular and registers many tens of thousands
of hit monthly. His papers outlining his algorithms are
cited almost every day of the year.
Applications:
- Hybridization of two different strands of DNA or RNA
Computations consider 5 different ensembles of structures. Partition function calculations are performed for the heterodimer, the two possible homodimers, and for folding of both single strand. Ensemble free energies are computed, leading to simulation of heat capacity, Cp, as a function of temperature. Base pair probabilities are computed and combined with published extinction coefficients to simulate UV absorbance as a function of temperature.
- Homodimer simulations
This simulation considers both the folding and dimerization of one single-stranded DNA or RNA molecule.
- Two-state melting (hybridization)
One RNA or DNA dimer structure versus random coil.
- Two-state melting (folding)
The classical two-state melt: one RNA or DNA folded structure versus random coil.
- Quikfold
Structures and energies for a number of sequences.
- Zipfold
Free energy only for a number of sequences.
References:
Nucleic Acids Research published an article on the DINAMelt server in July 2005. This and other relevant citations may be found on the references page.
Software:
The DINAMelt servers are powerd by a software package named "UNAFold", developed by Markham and Zuker at RPI. For non-commercial use, UNAFold may be downloaded from this web site. Commercial use requires a special license; see here for details.
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