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Deformational dynamics and nmr relaxation of supercoiled DNAs
Author(s) -
Langowski Jörg,
Fujimoto Bryant S.,
Wemmer David E.,
Benight Albert S.,
Drobny Gary,
Shibata John H.,
Schurr J. Michael
Publication year - 1985
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360240609
Subject(s) - chemistry , relaxation (psychology) , anisotropy , rigidity (electromagnetism) , fluorescence anisotropy , molecular physics , crystallography , nuclear magnetic resonance , optics , physics , quantum mechanics , psychology , social psychology , biochemistry , membrane
The conformation and internal dynamics of supercoiled pUC 8 DNA (2717 bp) are examined by dynamic light scattering, and the magnitude and uniformity of its torsional rigidity are determined using time‐resolved fluorescence polarization anisotropy of intercalated ethidium dye. Neither measurement gives any indication of an appreciably reduced bending or twisting rigidity, or anomalously rapid internal motions. For 31 P, in supercoiled pUC 8, we measure T 2 = (2.0 ± 0.5) × 10 −3 s. This lies within the range of present theoretical estimates obtained using normal rigidities. The proton linewidths observed for pUC 8 and pBR322 (4363 bp) DNAs are within a factor of 2–3 of those similarly estimated assuming ordinary rigidities. According to Bendel, Laub and James [(1982) J. Am. Chem. Soc. 104 , 6748–6754], supercoiled pIns36 DNA (7200 bp) exhibits an astonishingly long T 2 = 1.17 s for 31 P, a slowest rotational relaxation time, τ = 5 × 10 −9 s, and an enormously reduced bending rigidity. Serious questions raised by these findings are examined here. The 5 × 10 −9 s slowest rotational relaxation time is shown to be physically inadmissible. The nmr relaxation theory developed previously by Allison, Shibata, Wilcoxon, and Schurr [(1982) Biopolymers 21 , 729–762], is modified to incorporate new results for deformable filaments, which directly introduce the highly nonexponential tumbling correlation function for reorientation of the local helix axis. Essential requirements for a complete calculation of R 2 , including estimation of the tumbling correlation function and evaluation of the still unknown DIP/CSA cross‐term, are described in detail. Slow coil‐deformation modes analogous to the Rouse‐Zimm modes of linear DNAs are shown to make an important, if not dominant, contribution to the R 2 relaxation rate. Geometrical parameters in the theory are chosen to provide good agreement with literature data for 600‐bp linear DNA. Using this theory and an informed guess for the tumbling correlation function, we find that the 31 P‐nmr relaxation data of Bendel et al., if correct, necessarily impose on their DNA one or more extreme properties, such as enormously reduced bending or twisting rigidities. In contrast, the same theory yields reasonable agreement with the T 2 reported here for 31 P in supercoiled pUC 8 DNA when its rigidities are assumed to be quite ordinary.