NMR distance measurements in DNA duplexes: sugars and bases have the same correlation times
- 1 December 1989
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 28 (26) , 10001-10007
- https://doi.org/10.1021/bi00452a019
Abstract
To evaluate whether the sugar moieties of short DNA duplexes exhibit local motion of sufficient amplitude to affect interproton distance measurements, we have carried out a series of time-dependent NOESY experiments at increasingly shorter mixing times on dodecamer DNA duplexes. By use of the cytosine H5-H6 vector as a known distance in the bases and the geminal 2''H-2''''H vector as a known distance in the sugars, the corresponding apparent cross-relaxation rates were sampled at various mixing times. While the ratio of the inverse sixth power of these two fixed distances is in the range 6-7, when the system is sampled at 100 ms the apparent initial rate of growth of the 2''H-2''''H NOESY crosspeak is only 1.9-2.0 times faster than that of the H5-H6 crosspeak.sbd.in agreement with the results of Clore and Gronenborn [Clore, G.M., and Gronenborn, A. M. (1984) FEBS Lett. 172, 219; (1984) FEBS Lett. 175, 117] and of Gronenborn and Clore [Gronenborn A.M., and Clore, G. M. (1985) Prog. NMR Spectrosc. 17, 1]. This observation was interpreted to indicate the existence of internal mobility with a 3-fold shorter correlation time for the sugar moieties in DNA and led to the use of this shorter correlation time to estimate sugar-sugar proton distances and many sugar-base proton distances in subsequent DNA structure determination. We have examined 2''H-2''''H cross-relaxation and H5-H6 cross-relaxation at 100, 90, 60, 30, and 15 ms in dodecamer DNA duplexes. The ratio of the rates increases smoothly from 1.9-2.0 to 6-7 as the mixing time is reduced. The results show that the scaling discrepancy at 100 ms is not due to internal motion in the sugar but is simply due to spin diffusion from the rapidly relaxing 2''H,2''''H germinal protons. The lack of significant large-amplitude nanosecond local motion in the sugars casts doubt on the accuracy of interproton distances measured on the assumption of a 3-fold shorter correlation time for sugar protons and hence on the validity of DNA structures generated from such distances.This publication has 18 references indexed in Scilit:
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