Proton Nuclear Magnetic Resonance Study of a Self-Complementary Decadeoxyribonucleotide, C-C-A-A-G-C-T-T-G-G

A short DNA helix, d-(C-C-A-A-G-C-T-T-G-G)₂, has been thoroughly investigated by ¹H NMR spectroscopy. All 17 nonexchangeable base proton resonances have been assigned by the aid of the assigned ¹H NMR spectra of two half-decamer molecules (C-C-A-A-G and C-T-T-G-G) [Cheng, D. M., Kan, L.-S., Leutzinger, E. E., Jayaraman, K., Miller, P. S., & Ts'o, P. O. P. (1982) Biochemistry 21, 621] and their equimolar mixture at high temperature. The five NH-N hydrogen-bonded resonances were assigned by a thermal perturbation procedure as well as by nuclear Overhauser effects (NOE) from the already assigned base protons. These assignment procedures can be adopted as a guide for the assignment of the base proton resonances in other short helices comprised of 6–15 nucleotidyl units. The assigned nonexchangeable proton resonances at high temperature were carefully followed to low temperature and gave sigmoid curves indicative of cooperative helix to coil transitions. The assignment of H_1′ proton resonances in the helical state was made from the assigned base proton resonances with the application of double resonance techniques and NOE experiments. The analysis of the sugar puckering conformation of this helix can be estimated from the well-resolved resonances of H_1′. All the nucleotidyl residues of the helix are predominantly in the C_2′-endo form within a range of graded variation of 66–87% starting from the terminal nucleotides to residues toward the center residue of the helix. Thus, the circular dichroism data [Miller, P. S., Cheng, D. M., Dreon, N., Jayaraman, K., Kan, L.-S., Leutzinger, E. E., Pulford, S. M., & Ts'o, P. O. P. (1980) Biochemistry 19, 4688] and the sugar conformational analyses strongly indicate that this short DNA helix assumes a conformation in aqueous solution similar to but not necessarily identical with the B form. The through-space magnetic field effects on the base protons and NH-N protons in the helices were calculated and compared with the observed values. This comparison indicates that for the base protons, application of both ring-current effects and atomic anisotropic effects is preferred but for the NH-N protons the application of ring-current effect alone is preferred over the application of both ring-current effects and atomic anisotropic effects. The usefulness of the polarization effect remains to be further evaluated. The computed values, derived from the best theoretical treatment cited above, do support the conclusion that this helix assumes a B conformation. With all the resonances of the base protons, H_1′ protons, and NH-N protons individually and reliably assigned, this stable decameric DNA helix can serve as an effective model system for the testing of NMR theory and application to nucleic acid research.