DNA fragment conformations IV - Helix-coil transition and conformation of d-CCATGG in aqueous solution by 1H-NMR spectroscopy

Abstract

The helix-coil transition and conformation of d-CCATGG were investigated using 1H-NMR spectroscopy at various frequencies (90, 276, 400 MHz). The changes in the chemical shifts and linewidths of imino protons between 5 degrees and 35 degrees C show that the d-CCATGG fraying process consists of two stages: the external dC.dG base pairs open at first, th internal dC.dG and central dA.dT base pairs then open simultaneously at higher temperatures similar to the case of d-ACATGT. The midpoint temperatures, the helix and coil proportions and the dissociation constant were determined from the sigma = f(t degree) curves of the base and sugar protons. The results indicate that the midpoint temperature increases with the number of the dG.dC base pair in a given size sequence, while the dissociation enthalpy appears to be independent. The difference between the T1 value of a base proton of the external and internal residues of the same nature is found to be a good criterion for base proton assignment. The high predominance of the S conformation for all residues shows that d-CCATGG duplexes adopt the B-helical conformation.