NMR studies of alkali metal ion binding in G-quadruplex DNA and model systems

            DNA oligomers containing repeats of guanine (G) can fold into four-stranded structures called G-quadruplexes. In the human genome, there are several G-rich regions where a G-quadruplex structure may potentially form. Among them, the telomere found at the termini of eukaryotic chromosomes is of particular importance. During normal cell division, telomeric DNA sequences shorten incrementally and such a cumulative loss eventually becomes lethal to somatic cells. An enzyme known as telomerase is capable of rebuilding the ends of telomeres. More importantly, this enzyme is found active in 85-90% of proliferating tumour cells but inactive in somatic cells. In the past decade, a tremendous amount of efforts have been devoted by scientists to the understanding of the relationship between cell immortalization in tumour cells and the maintenance of telomere length.² Because the G-quadruplex structure may be a key feature of telomeres in vivo, it is of fundamental importance to understand all aspects of G-quadruplex formation and its binding to proteins.

            It is known that the presence of alkali metal ions such as K⁺ and Na⁺ is critical in the formation, stability and function of G-quadruplex DNA structures. Structural details regarding the mode of ion binding in G-quadruplex DNA have come primarily from X-ray crystallographic studies. Recently, we have made a breakthrough in this area. In particular, we have successfully identified the ²³Na, ³⁹K, ⁸⁷Rb and ⁴³Ca NMR spectral signatures for Na⁺, K⁺, Rb⁺ and Ca²⁺ ions bound to the G-quadruplex structure. We have applied this new solid-state NMR method to determine the number and coordination of Na⁺ ions in a telomeric DNA sequence from Oxytricha nova, d(G₄T₄G₄). This work represents the first time that a technique other than crystallography has yielded site-specific information about Na⁺ ion coordination in G-quadruplex DNA. Currently, we are extending our novel NMR methodologies to study telomeric DNAs and their protein complexes.

Our publications in this area

1.        R. Ida and G. Wu,  Journal of the American Chemical Society 130, 3590-3602 (2008).
2.        I. C. M. Kwan, A. Wong, Y.-M. She, M. E. Smith, and G. Wu, Chemical Communications 682-684 (2008). (Featured on the front cover)
3.        R. Ida, I. C. M. Kwan, and G. Wu, Chemical Communications 795-797 (2007).
4.        A. Wong, R. Ida and G. Wu, Biochemical and Biophysical Research Communications 337, 363-366 (2005).
5.        R. Ida and G. Wu, Chemical Communications 4294-4296 (2005).
6.        A. Wong, R. Ida, L. Spindler, and G. Wu, Journal of the American Chemical Society 127, 6990-6998 (2005).
7.        G. Wu and A. Wong, Biochemical and Biophysical Research Communications  323, 1139-1144 (2004).
8.        A. Wong and G. Wu, Journal of the American Chemical Society 125, 13895-13905 (2003).
9.        G. Wu, A. Wong, Z. Gan, and J. T. Davis, Journal of the American Chemical Society 125, 7182-7183 (2003).
10.      A. Wong, J. Fettinger, S. L. Forman, J. T. Davis, and G. Wu, Journal of the American Chemical Society 124, 742-743 (2002).
11.      G. Wu and A. Wong, Chemical Communications 2658-2659 (2001).

Solid-state ¹⁷O NMR for organic and biological compounds

            Oxygen is one of the most important elements in organic and biological molecules. Solid-state ¹⁷O (spin-5/2) NMR has, however, remained largely unexplored due to experimental difficulties in detecting NMR signals for quadrupolar nuclei. Given the fact that numerous NMR studies have been carried out for ¹H, ¹³C and ¹⁵N, ¹⁷O can be considered as the last frontier of biomolecular NMR spectroscopy. In the past several years, we have developed a comprehensive research program on solid-state ¹⁷O NMR studies of organic and biological compounds. We have first synthesized a series of ¹⁷O-labeled compounds containing various functional groups, and then characterized their solid-state ¹⁷O NMR properties. Most of the functional groups that we examined had no solid-state ¹⁷O NMR data available before our studies. We have also applied for the first time ¹⁷O multiple-quantum magic-angle spinning (MQMAS) technique to organic compounds and obtained high-resolution ¹⁷O NMR spectra where different oxygen sites can be resolved. The most intriguing aspect of ¹⁷O NMR is the remarkable sensitivity of ¹⁷O NMR parameters (both chemical shift and quadrupole coupling tensors) to hydrogen bonding interaction. We are currently expanding our effort in the development and application of solid-state ¹⁷O NMR with an emphasis on biological molecules.

Our publications in this area

1.         I. C. M. Kwan, X. Mo, and G. Wu, Journal of the American Chemical Society 129, 2397-2409 (2007).
2.         R. Ida, M. De Clerk, and G. Wu, Journal of Physical Chemistry Part A 110, 1065-1071 (2006).
3.         G. Wu and K. Yamada, Solid State Nuclear Magnetic Resonance 24, 196-208 (2003).
4.         G. Wu, S. Dong, R. Ida, and N. Reen, Journal of the American Chemical Society 124, 1768-1777 (2002).
5.         G. Wu and S. Dong, Journal of the American Chemical Society 123, 9119-9125 (2001).
6.         G. Wu, S. Dong, and R. Ida, Chemical Communications 891-892 (2001).
7.         S. Dong, R. Ida, and G. Wu, Journal of Physical Chemistry Part A 104, 11194-11202 (2000).
8.          K. Yamada, S. Dong, and G. Wu. Journal of the American Chemical Society 122, 11602-11609 (2000).
9.         G. Wu, A. Hook, S. Dong, and K. Yamada. Journal of Physical Chemistry Part A 104, 4102-4107 (2000).
10.       G. Wu, K. Yamada, S. Dong, and H. Grondey. Journal of the American Chemical Society 122, 4215-4216 (2000).
11.        S. Dong, K. Yamada, and G. Wu. Z. Naturforsch. 55A, 21-28 (2000).