DNA duplex melting monitored via lineshape analysis of 1H NMR spectra

Václav Římal1, Helena Štěpánková1, Josef Štěpánek2


Charles University in Prague, Faculty of Mathematics and Physics,

1 Department of Low-Temperature Physics, V Holešovičkách 2, 180 00 Prague 8, Czech Republic

2 Institute of Physics, Ke Karlovu 5, 121 16 Prague 2, Czech Republic



Structural stability of DNA double-helix plays an important role in many biological processes. Nuclear magnetic resonance is capable to provide a detailed insight into the temperature induced base-pair breaking and corruption of regular geometry at particular location of DNA chain. This application requires (in the case of 1H spectra and stationary magnetic field > 7 T) the set of temperature dependent NMR spectra to be analyzed in respect to effect of chemical exchange between the duplex and single-strand states on NMR lineshape. By solving set of Bloch-McConnell differential equations for the case of free induction decay, we have found an analytical formula for the spectral lineshape in the case of chemical exchange between unequally populated states with different relaxation rates. This allows the experimental spectra to be straightly fitted by this expression without long-term numerical calculations. This approach was applied to NMR spectra of aromatic protons in self-complementary DNA octamers, d(GATGCATC) and d(CTTGCAAG), measured in a broad temperature range covering the duplex melting. For every nucleobase we obtained independently temperature profiles of the equilibrium constant and the kinetic association constant. These characteristics were found as sensitive indicators of local deviations from the overall duplex properties.

Key words

Structural stability of DNA duplex, proton NMR spectroscopy, chemical exchange