Users of the DINAMelt Server are requested to cite:

Markham, N. R. & Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res., 33, W577-W581.
[Abstract] [FREE Full Text] [Print PDF] [Screen PDF] [Supplementary Material]

Markham, N. R. & Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Function and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3–31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.
[Abstract] [Full Text] [PDF]

Other articles that may be relevant include:

Dimitrov, R. A. & Zuker, M. (2004) Prediction of hybridization and melting for double-stranded nucleic acids. Biophys. J., 87, 215-226.
[Abstract] [Full Text] [PDF]

SantaLucia, Jr., J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA, 95, 1460-1465.
[Abstract] [Full Text] [PDF]

Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H. & Zuker, M. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. USA, 91, 9218-9222.
[Abstract] [Full Text] [PDF]

Mathews, D. H., Sabina, J., Zuker, M. and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.