Electric birefringence of restriction enzyme fragments of DNA: Optical factor and electric polarizability as a function of molecular weight

Stellwagen, Nancy C.

doi:10.1002/bip.1981.360200302

Cited by 152 publications

(117 citation statements)

References 79 publications

(28 reference statements)

Supporting

Mentioning

104

Contrasting

Unclassified

Order By: Relevance

“…For S ≫ a the model leads to an approximately quadratic dependence of ∆α with S. This can be noted in Figure 2, where experimental data of ∆α are represented versus S 2 and S 2 − Sa . These experimental values of ∆α and S were reported by others authors 19,20,1 in an independent way. The data used correspond to chain lengths Figure 2, the values of S 2 − Sa were calculated estimating a equal to 34 Å.…”

Section: Electric Polarizability Tensorsupporting

confidence: 83%

“…There exist, in the bibliography, experimental data of electric polarizability anisotropy reported by other authors. 19,20,1 Of course, these data do not come from direct measurements but from the analysis of the birefringence and dichroism measurements and from their interpretation in the basis of a rod-like polyelectrolyte model. The anisotropy of electric polarizability obtained in this way rises with the chain length.…”

Section: Electric Polarizability Tensormentioning

confidence: 99%

See 1 more Smart Citation

Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

Bertolotto

Umazano

2016

AIP Advances

View full text Add to dashboard Cite

In the present work we make a theoretical study of the steady state electric linear dichroism of DNA fragments in aqueous solution. The here developed theoretical approach considers a flexible bent rod model with a saturating induced dipole moment. The electric polarizability tensor of bent DNA fragments is calculated considering a phenomenological model which theoretical and experimental backgroung is presented here. The model has into account the electric polarizability longitudinal and transversal to the macroion. Molecular flexibility is described using an elastic potential. We consider DNA fragments originally bent with bending fluctuations around an average bending angle. The induced dipole moment is supposed constant once the electric field strength grows up at critical value. To calculate the reduced electric linear dichroism we determine the optical factor considering the basis of the bent DNA perpendicular to the molecular axis. The orientational distribution function has into account the anisotropic electric properties and the molecule flexibility. We applied the present theoretical background to fit electric dichroism experimental data of DNA fragments reported in the bibliography in a wide range of molecular weight and electric field. From these fits, values of DNA physical properties are estimated. We compare and discuss the results here obtained with the theoretical and experimental data presented by other authors. The original contributions of this work are: the inclusion of the transversal electric polarizability saturating with the electric field, the description of the electric properties with an electric polarizability tensor dependant on the bending angle and the use of an arc model originally bent.

show abstract

Section: Electric Polarizability Tensorsupporting

confidence: 83%

Section: Electric Polarizability Tensormentioning

confidence: 99%

Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

Bertolotto

Umazano

2016

AIP Advances

View full text Add to dashboard Cite

show abstract

“…The fragments were extracted from the gel slices using Qiagen's QIAquick Gel Extraction Kit (centrifuge protocol), and purified and desalted by adsorption on either the Qiagen columns in the kit or small (diethylamine) ethyl (DEAE) columns, using methods described previously. 36 The results were independent of the method used to purify the fragments. The fragments were then eluted into the desired buffer, the concentration determined by absorbance measurements as described above, and the stock solutions stored at Ϫ20°C until needed.…”

mentioning

confidence: 98%

DNA persistence length revisited

2002

Self Cite

View full text Add to dashboard Cite

DNA restriction fragments ranging from 79 to 789 base pairs in length have been characterized by transient electric birefringence (TEB) measurements at various temperatures between 4 and 43 degrees C. The DNA fragments do not contain runs of four or more adenine residues in a row and migrate with normal electrophoretic mobilities in polyacrylamide gels, indicating that they are not intrinsically curved or bent. The low ionic strength buffers used for the measurements contained 1 mM Tris Cl, pH 8.0, EDTA, and variable concentrations of Na(+) or Mg(2+) ions. The rotational relaxation times were obtained by fitting the TEB field-free decay signals with a nonlinear least-squared fitting program; the decay of the birefringence was monoexponential for fragments < or = 241 base pair (bp) in length and multiexponential for larger fragments. The terminal relaxation times, characteristic of the end-over-end rotation of the DNA molecules, were then used to determine the persistence length (p) and hydrodynamic radius (r) of DNA as a function of temperature and ionic strength, using several different hydrodynamic models. The specific values obtained for p and r are model dependent. The wormlike chain model of P. J. Hagerman and B. H. Zimm (Biopolymers 1981, Vol. 20, pp. 1481-1502) combined with the revised Broersma equation (J. Newman et al., Journal of Mol Biol 1997, Vol. 116, pp. 593-606) appears to be the most suitable for describing the flexibility of DNA in low ionic strength solutions. The values of p and r obtained from the global least squares fitting of this equation are independent of DNA length, and the deviations of the individual values from the average are reasonably small. The consensus r value calculated for DNA in various low ionic strength solutions containing 1 mM Tris buffer is 14.7 +/- 0.4 A at 20 degrees C. The consensus p values decrease from 814 approximately 564 A in solutions containing 1 mM Tris buffer plus 0.2-1 mM NaCl and decrease still further to 440 A in solutions containing 0.2 mM Mg(2+) ions. The persistence length exhibits a shallow maximum at 20 degrees C and decreases slowly upon either increasing or decreasing the temperature, regardless of the model used to fit the data. By contrast, the consensus values of the hydrodynamic radius are independent of temperature. The calculated persistence lengths and hydrodynamic radii are compared with other data in the literature.

show abstract

“…The short, monodisperse DNA samples in small quantities are now available conveniently by fragmenting either high molecular weight plasmid 5 or A.-phage 6 DNA with restriction enzymes, but the use of these fragmented samples in large amounts for hydrodynamic studies is prohibitive. The only practical method for preparing desired lower molecular weight DNA samples is the ultrasonic scission of a large amount of a high molecular DNA sample in a single batch.…”

mentioning

confidence: 99%

Ultrasonic Scission of Deoxyribonucleic Acid in Aqueous Solution III. The Solution Properties of Sonicated Low Molecular Weight Samples as Revealed by Light Scattering and Viscosity

Fukudome

Yamaoka

Ochiai

1987

Polym J

View full text Add to dashboard Cite

ABSTRACT:The light scattering and viscosity measurements were carried out at 25oC in 0.2 M NaCI solutions for 14 fractionated low molecular weight DNA (sDNA) samples, which were prepared by the precipitational fractionation of the sonicated calf thymus DNA fragments. The relationship between the intrinsic viscosity I'll and the weight-average molecular weight Mw could be expressed with an empirical formula, 1'1l=9.54x in cm 3 g-1 for 1.2x 10 5 ::;Mw::;3x 10 5 , but a sigmoidal change followed with an inflection region (3 x 10 5 ::; M w ::;6 x 10 5 ). The z-averaged square radius of gyration (S 2 ), was also determined from the angular dependence of scattered light intensity for each sDNA sample. The dependence of (S 2 ), and I'll on Mw was calculated theoretically at various values of the persistence length for the A-and B-ONA conformations. It was found that the effect of the polydispersity on (S 2 ), and I'll is important, if a quantitative comparison is made between the observed and calculated quantities.KEY WORDS Sonicated DNA I Molecular Weight I Light Scattering I Intrinsic Viscosity I Mean Radius of Gyration IIn the study of the hydrodynamic property of DNA in solution, the flexibility of the double-helical chain is the major factor which must always be considered. The flexibility is quantitatively expressed by the persistence length q. 1 -3 In order to evaluate the q value accurately, the molecular weight dependence of the mean square radius of gyration

~~show abstract~~

Electric birefringence of restriction enzyme fragments of DNA: Optical factor and electric polarizability as a function of molecular weight

Cited by 152 publications

References 79 publications

Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

DNA persistence length revisited

Ultrasonic Scission of Deoxyribonucleic Acid in Aqueous Solution III. The Solution Properties of Sonicated Low Molecular Weight Samples as Revealed by Light Scattering and Viscosity

Contact Info

Product

Resources

About