Water molecule binding and lifetimes on the DNA duplex d(CGCGAATTCGCG)2

Abstract

Measurements of the water proton spin-lattice relaxation rate for aqueous solutions of the palindromic dodecamer, d(CGCGAATTCGCG)2, are reported as a function of the magnetic field strength. The magnitude of the relaxation rates at low magnetic field strengths and the shape of the relaxation dispersion curve permit assessment of the number of water molecules which may be considered bound to the DNA for a time equal to or longer than the rotational correlation time of the duplex. The data are examined using limiting models that arbitrarily use the measured rotational correlation time of the polynucleotide complex as a reference point for the water molecule lifetime. If it is assumed that water molecules are bound at DNA sites for times as long as or longer than the rotational correlation time of the duplex, then the magnitude of the relaxation rates at low field require that there may be only two or three such water sites. However, if the lifetime constraint is relaxed, and we assume that the number of water molecules bound to the DNA is more nearly the number identified in the X-ray structures, then the average water molecule lifetime is on the order of 1 ns. Measurements of 1H NOESY spectra demonstrate that some water molecules must have lifetimes sufficiently long that negative Overhauser effects are observed. Taken together, these results suggest a distribution of water molecule lifetimes in which most of the DNA-bound water molecule lifetimes are shorter than the rotational correlation time of the duplex, but where some have lifetimes of at least 1 ns under these concentrated conditions.

Kinetics of DNA hydration

“…Within the overlapping range, 1 to 30 MHz, both studies reveal a dispersion with an amplitude much smaller than usually found for proteins. In contrast to Zhou & Bryant (1996), we argue that this dispersion is due to labile DNA protons rather than to long-lived water molecules. In particular, our ®nding that netropsin binding does not eliminate this dispersion (Figure 11), conclusively demonstrates that it cannot be due to water molecules in the minor groove.…”

“…Finally, we comment on a 1 H NMRD and NOESY study, of the same dodecamer as studied here, that appeared in print after the completion of this work (Zhou & Bryant, 1996). The 1 H NMRD pro®le reported by these authors extends up to 30 MHz, as compared to 600 MHz here.…”

“…This dispersion appears to be due to internal motion at DNA sites containing labile protons. The 1 H dispersion therefore provides very little information about DNA hydration, despite recent claims to the contrary (Zhou & Bryant, 1996).…”

Model-Free Analysis of Stretched Relaxation Dispersions

“…[29], the integral of J() is generally larger than that of the reference Lorentzian, so that 0 Ն ͗ C ͘.…”

Multinuclear Relaxation Dispersion Studies of Protein Hydration

“…Well-documented cases include a study of poly (methacrylic acid) (Glasel, 1970) and a recent study of an oligonucleotide (Zhou and Bryant, 1996). In both cases, subsequent studies revealed that the relaxation effects that had been attributed to hydration water were entirely due to labile hydrogens (Halle and Piculell, 1982;Denisov et al, 1997a).…”