title: NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA.
abstract: The conformational exchange of the phosphate and deoxyribose groups of the DNA oligomers d(GCGTACGC)(2) and d(CGCTAGCG)(2) have been investigated using a combination of homonuclear and heteronuclear NMR techniques. Two-state exchange between phosphate B(I) and B(II) conformations and deoxyribose N and S conformations was expressed as percent population of the major conformer, %B(I) or %S. Sequence context-dependent variations in %B(I) and %S were observed. The positions of the phosphate and deoxyribose equilibria provide a quantitative measure of the ps to ns timescale dynamic exchange processes in the DNA backbone. Linear correlations between %B(I), %S, and previously calculated model free (13)C order parameters (S(2)) were observed. The %B(I) of the phosphates were found to be correlated to the S(2) of the flanking C3' and C4' atoms. The %B(I) was also found to be correlated with the %S and C1' S(2) of the deoxyribose ring 5' of the phosphates. The %B(I) of opposing phosphates is correlated, while the %B(I) of sequential phosphates is anti-correlated. These correlations suggest that conformational exchange processes in DNA are coupled to each other and are modulated by DNA base sequence, which may have important implications for DNA-protein interactions.
authors.affiliation: Department of Molecular and Cellular Biochemistry Department of Chemistry, & Kentucky Center for Structural Biology, University of Kentucky, Lexington, KY 40536-0084, USA.
authors.forename: R J
authors.initials: RJ
authors.lastname: Isaacs
authors.forename: H P
authors.initials: HP
authors.lastname: Spielmann
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D003855:Deoxyribose / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010710:Phosphates / Q000737:chemistry / Q000378:metabolism*; D011522:Protons; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D009838:Oligodeoxyribonucleotides; D010710:Phosphates; D011522:Protons; D003855:Deoxyribose; D004247:DNA