Abstract
A simple thermal melting experiment may be used to demonstrate the stabilization of a given structure by a ligand (usually a small molecule, sometimes a peptide). Preparation of the sample is straightforward, and the experiment itself requires an inexpensive apparatus. Furthermore, reasonably low amounts of sample are required. A qualitative analysis of the data is simple: An increase in the melting temperature (T m) indicates preferential binding to the folded form as compared to the unfolded form. However, it is perilous to derive an affinity constant from an increase in T m as other factors play a role.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Stewart CR (1968) Broadening by acridine orange of the thermal transition of DNA. Biopolymers 6:1737-1743
Mergny JL, Duval-Valentin G, Nguyen CH, Perroualt L, Faucon B, Montenay-Garestier T, Bisagni E, Hélène C (1992) Triple helix specific ligands. Science 256:1691-1694
Escudé C, Nguyen CH, Mergny JL, Sun JS, Bisagni E, Garestier T, Hélène C (1995) Selective stabilization of DNA triple helices by benzopyridoindole derivatives. J Am Chem Soc 117:10212-10219
Crothers DM (1971) Statistical thermodynamics of nucleic acids melting transitions with coupled binding equilibria. Biopolymers 10:2147-2160
McGhee JD (1976) Theoretical calculation of the helix-coil transition of DNA in the presence of large, cooperatively binding ligands. Biopolymers 15:1345-1375
McGhee JD, von Hippel PH (1974) Theoretical aspects of DNA Protein interactions: Cooperative and non cooperative binding of large ligands to a one dimensional homogeneous lattice. J Mol Biol 86:469-489
Mergny JL, Phan AT, Lacroix L (1998) Following G-quartet formation by UV-spectroscopy. FEBS Lett 435:74-78
De Cian A, Mergny JL (2007) Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation. Nucleic Acids Res 35:2483-2493
Mergny JL, Boutorine AS, Garestier T, Belloc F, Rougée M, Bulychev NV, Koshkin AA, Bourson J, Lebedev AV, Valeur B, Thuong NT, Hélène C (1994) Fluorescence energy transfer as a probe for nucleic acid structures and sequences. Nucleic Acids Res 22:920-928
Simonsson T, Sjoback R (1999) DNA tetraplex formation studied with fluorescence resonance energy transfer. J Biol Chem 274:17379-17383
Mergny JL (1999) Fluorescence energy transfer as a probe for tetraplex formation: The i-motif. Biochemistry 38:1573-1581
Mergny JL, Maurizot JC (2001) Fluorescence resonance energy transfer as a probe for G-quartet formation by a telomeric repeat. Chembiochem 2:124-132
Rachwal PA, Fox KR (2007) Quadruplex melting. Methods 43:291-301
De Cian A, Guittat L, Kaiser M, Sacca B, Amrane S, Bourdoncle A, Alberti P, Teulade-Fichou MP, Lacroix L, Mergny JL (2007) Fluorescence-based melting assays for studying quadruplex ligands. Methods 42:183-195
Darby RAJ, Sollogoub M, McKeen C, Brown L, Risitano A, Brown N, Barton C, Brown T, Fox KR (2002) High throughput measurement of duplex, triplex and quadruplex melting curves using molecular beacons and a LightCycler. Nucleic Acids Res 30:e39
Schultes CM, Guyen W, Cuesta J, Neidle S (2004) Synthesis, biophysical and biological evaluation of 3, 6-bis-amidoacridines with extended 9-anilino substituents as potent G-quadruplex-binding telomerase inhibitors. Bioorg Med Chem Lett 14:4347-4351
Gomez D, Paterski R, Lemarteleur T, Shin-ya K, Mergny JL, Riou JF (2004) Interaction of telomestatin with the telomeric single-strand overhang. J Biol Chem 279:41487-41494
Juskowiak B, Galezowska E, Zawadzka A, Gluszynska A, Takenaka S (2006) Fluorescence anisotropy and FRET studies of G-quadruplex formation in presence of different cations. Spectrochim Acta A Mol Biomol Spectrosc 64:835-843
Moore MJB, Schultes CM, Cuesta J, Cuenca F, Gunaratnam M, Tanious FA, Wilson WD, Neidle S (2006) Trisubstituted acridines as G-quadruplex telomere targeting agents. Effects of extensions of the 3, 6-and 9-side chains on quadruplex binding, telomerase activity, and cell proliferation. J Med Chem 49:582-599
Sapsford KE, Berti L, Medintz IL (2006) Materials for fluorescence resonance energy transfer analysis: Beyond traditional donor-acceptor combinations. Angew Chem Int Ed Engl 45:4562-4589
De Cian A, Grellier P, Mouray E, Depoix D, Bertrand H, Monchaud D, Teulade-Fichou MP, Mergny JL, Alberti P (2008) Plasmodium telomeric sequences: Structure, stability and quadruplex targeting by small compounds. Chembiochem 9:2730-2739
De Cian A, Gros J, Guédin A, Haddi M, Lyonnais S, Guittat L, Roiu J-F, Trentesaux C, Sacca B, Lacroix L, Alberti P, Mergny LJ (2008) DNA and RNA quadruplex ligands. Nucleic acids Symp Ser 52:7-8
Juskowiak B, Takenaka S (2006) Fluorescence resonance energy transfer in the studies of guanine quadruplexes. Methods Mol Biol 335:311-341
Cantor CR, Warshaw MM, Shapiro H (1970) Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 9:1059-1077
Mergny JL, Lacroix L, Teulade-Fichou MP, Hounsou C, Guittat L, Hoarau M, Arimondo PB, Vigneron JP, Lehn JM, Riou JF, Garestier T, Hélène C (2001) Telomerase inhibitors based on quadruplex ligands selected by a fluorescent assay. Proc Natl Acad Sci USA 98:3062-3067
Gros J, Guédin A, Mergny JL, Lacroix L (2008) G-quadruplex formation interferes with P1 helix formation in the RNA component of telomerase hTERC. Chembiochem 9:2075-2078
Kaiser M, Sainlos M, Lehn JM, Bombard S, Teulade-Fichou MP (2006) Aminoglycoside-quinacridine conjugates: Towards recognition of the P6.1 element of telomerase RNA. Chembiochem 7:321-329
Rachwal PA, Findlow S, Werner JM, Brown T, Fox KR (2007) Intramolecular DNA quadruplexes with different arrangements of short and long loops. Nucleic Acids Res 35:4214-4222
Gros J, Rosu F, Amrane S, De Cian A, Gabelica V, Lacroix L, Mergny JL (2007) Guanines are a quartet’s best friend: Impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes. Nucleic Acids Res 35:3064-3075
Mergny JL, Lacroix L (2003) Analysis of thermal melting curves. Oligonucleotides 13:515-537
Mergny JL, Lacroix L, Han X, Leroy JL, Hélène C (1995) Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. J Am Chem Soc 117:8887-8898
Fukada H, Takahashi K (1998) Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. Proteins 33:159-166
Granotier C, Pennarun G, Riou L, Hoffschir F, De Cian A, Gomex D, Mandine E, Riou JF, Mergny JL, Mailliet P, Duttrilaux P, Boussin FD (2005) Preferential binding of a G-quadruplex ligand to human chromosome ends. Nucleic Acids Res 33:4182-9410
Pennarun G, Granotier C, Hoffschir F, Mandine E, Biard D, Gauthier LR, Boussin FD (2008) Role of ATM in the telomere response to the G-quadruplex ligand 360A. Nucleic Acids Res 36:1741-1754
Acknowledgments
We thank all the past and present members of the “Laboratoire de Biophysique” in the Muséum National d’Histoire Naturelle. This work was supported by an E.U. FP6 “MolCancerMed” (LSHC-CT-2004-502943) grant.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Guédin, A., Lacroix, L., Mergny, JL. (2010). Thermal Melting Studies of Ligand DNA Interactions. In: Fox, K. (eds) Drug-DNA Interaction Protocols. Methods in Molecular Biology, vol 613. Humana Press. https://doi.org/10.1007/978-1-60327-418-0_2
Download citation
DOI: https://doi.org/10.1007/978-1-60327-418-0_2
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60327-417-3
Online ISBN: 978-1-60327-418-0
eBook Packages: Springer Protocols