Determination of distances involving exchangeable protons from NOESY spectra of two DNA dodecamers.
Two-dimensional proton nuclear Overhauser effect (NOESY) spectra were obtained as a function of mixing time for two DNA dodecamers, 5'-CGCGAATTCGCG-3' and 5'-CGCAAATTTGCG-3', in aqueous solutions. The time evolution of cross-peak volumes was quantitatively analyzed based on the approximate solution of the relaxation/exchange equation over a range of mixing times from 30 to 150 ms. Inter-proton distances, involving exchangeable protons in key locations of the structures, were calculated and compared to the distances predicted by the crystal structures. These NMR-derived distances enhance the number of constraints, and their accuracy, for determination of solution structures of the two DNA dodecamers.
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459.
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D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011522:Protons; D014867:Water
D009838:Oligodeoxyribonucleotides; D011522:Protons; D014867:Water; D004247:DNA