title: NMR distance measurements in DNA duplexes: sugars and bases have the same correlation times.
abstract: To evaluate whether the sugar moieties of short DNA duplexes exhibit local motion of sufficient amplitude to affect interproton distance measurements, we have carried out a series of time-dependent NOESY experiments at increasingly shorter mixing times on dodecamer DNA duplexes. By use of the cytosine H5-H6 vector as a known distance in the bases and the geminal 2'H-2''H vector as a known distance in the sugars, the corresponding apparent cross-relaxation rates were sampled at various mixing times. While the ratio of the inverse sixth power of these two fixed distances is in the range 6-7, when the system is sampled at 100 ms the apparent initial rate of growth of the 2'H-2''H NOESY crosspeak is only 1.9-2.0 times faster than that of the H5-H6 crosspeak--in agreement with the results of Clore and Gronenborn [Clore, G. M., & Gronenborn, A. M. (1984) FEBS Lett. 172, 219; (1984) FEBS Lett. 175, 117] and of Gronenborn and Clore [Gronenborn, A. M., & Clore, G. M. (1985) Prog. NMR Spectrosc. 17, 1]. This observation was interpreted to indicate the existence of internal mobility with a 3-fold shorter correlation time for the sugar moieties in DNA and led to the use of this shorter correlation time to estimate sugar-sugar proton distances and many sugar-base proton distances in subsequent DNA structure determination. We have examined 2'H-2"H cross-relaxation and H5-H6 cross-relaxation at 100, 90, 60, 30, and 15 ms in dodecamer DNA duplexes.(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Chemistry, University of Washington, Seattle 98195.
authors.forename: B R
authors.initials: BR
authors.lastname: Reid
authors.forename: K
authors.initials: K
authors.lastname: Banks
authors.forename: P
authors.initials: P
authors.lastname: Flynn
authors.forename: W
authors.initials: W
authors.lastname: Nerdal
mesh_terms: D001483:Base Sequence; D004247:DNA; D015246:Deoxyribonuclease EcoRI; D003855:Deoxyribose; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011089:Polydeoxyribonucleotides; D011522:Protons; D011687:Purines; D011743:Pyrimidines
chemical_list: D011089:Polydeoxyribonucleotides; D011522:Protons; D011687:Purines; D011743:Pyrimidines; D003855:Deoxyribose; D004247:DNA; D015246:Deoxyribonuclease EcoRI