Field- and Phage-Induced Dipolar Couplings in a Homodimeric DNA Quadruplex: Relative Orientation of G·(C-A) Triad and G-Tetrad Motifs and Direct Determination of C2 Symmetry Axis Orientation

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• 作者：Hashim M. Al-Hashimi ; Ananya Majumdar ; Andrey Gorin ; Abdelali Kettani ; Eugene Skripkin ; and Dinshaw J. Patel
• 刊名：Journal of the American Chemical Society
• 出版年：2001
• 出版时间：January 31, 2001
• 年：2001
• 卷：123
• 期：4
• 页码：633 - 640
• 全文大小：195K
• 年卷期：v.123,no.4(January 31, 2001)
• ISSN：1520-5126

文摘

We present a new NMR procedure for determining the three-dimensional fold of C2-symmetricnucleic acid homodimers that relies on long-range orientational constraints derived from the measurement oftwo independent sets of residual dipolar couplings under two alignment conditions. The application isdemonstrated on an ¹⁵N/¹³C-enriched deoxyoligonucleotide sequence, d(G-G-G-T-T-C-A-G-G), shownpreviously to dimerize into a quadruplex in solution and form a pair of G·(C-A) triads and G-G-G-G tetrads(G-tetrad) motifs. One-bond ¹H-¹⁵N (¹D_NH) and ¹H-¹³C (¹D_CH) residual dipolar couplings have been measuredbetween nuclei in the bases of these motifs using bacteriophage as an ordering medium, and under directmagnetic field alignment (800 MHz). By combining the two dipolar data sets in an order matrix analysis, theorientation of the G·(C-A) triad relative to the G-tetrad within a contiguous monomeric unit can directly bedetermined, even in the presence of interstrand/intrastrand NOE ambiguity. We further demonstrate that theorientation of the C2-axis of molecular symmetry in the homodimer relative to the G·(C-A) triad and G-tetradmotifs can unambiguously be determined using the two sets of independent dipolar coupling measurements.The three-dimensional fold of the homodimer determined using this procedure is very regular and in excellentagreement with a previously determined high-resolution NOE-based NMR structure, where interstrand/intrastrandNOEs were treated as ambiguous and where noncrystallographic symmetry constraints were implicitly imposedduring the structure calculation.