Proton Assignment Strategies in Nucleic Acid NMR Studies

Abstract

The last few years have seen a rapid expansion in our ability to study nucleic acids and proteins of increasing size and spectral complexity by high-resolution NMR spectroscopy (see Kearns. 1984. and Wemmer & Reid. 1985. for recent reviews). An important factor in our ability to study biopolymers in the 8.000 – 16.000 mol. wt. range is the sensitivity and resolution of modern NMR spectrometers with magnetic field strengths in the 11–12 Tesia range (ca. 500 MHz). Even at such frequencies, the NMR spectra of 10.000 dalton biopolymers are very crowded, with many overlapping resonances, and the introduction of two-dimensional NMR spectroscopy (2DNMR) has been an equally important development. As in all forms of spectroscopy, the ability to specifically assign the majority of resonance peaks is the first crucial step in any detailed study and 2DNMR has facilitated the ease and speed of assigning relatively complicated spectra. In this paper I shall present the techniques and strategies for assigning nucleic acid NMR spectra, with particular emphasis on short DNA molecules containing 10–20 base pairs. In presenting these assignment methods I shall draw on examples taken from the work of several members of my laboratory to whom I am grateful, particularly Dennis Hare. David Wemmer and Shan-Ho Chou.