Effects of Na<sup>+</sup> on the persistence length and excluded volume of T7 bacteriophage DNA

Sobel, E. S.; Harpst, J.A.

doi:10.1002/bip.360311311

Cited by 78 publications

(89 citation statements)

References 40 publications

(5 reference statements)

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“…Models which incorporate chain extensibility yield essentially the same P as those that do not, probably because the entropic and enthalpic components dominate the elastic behavior of the molecule in different parts of the F-x curve. The nonelectrostatic contribution dominates P at I Ͼ 20 mM, in accord with previous experimental determinations using light scattering (22) and flow birefringence (23) with phage DNA, and electro-optical measurements (24) with short (41-256 bp) DNA fragments.…”

Section: Persistence Lengthsupporting

confidence: 88%

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Ionic effects on the elasticity of single DNA molecules

Baumann

Smith

Bloomfield

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

923

111

996

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We used a force-measuring laser tweezers apparatus to determine the elastic properties of -bacteriophage DNA as a function of ionic strength and in the presence of multivalent cations. The electrostatic contribution to the persistence length P varied as the inverse of the ionic strength in monovalent salt, as predicted by the standard worm-like polyelectrolyte model. However, ionic strength is not always the dominant variable in determining the elastic properties of DNA. Monovalent and multivalent ions have quite different effects even when present at the same ionic strength. Multivalent ions lead to P values as low as 250-300 Å, well below the high-salt ''fully neutralized'' value of 450-500 Å characteristic of DNA in monovalent salt. The ions Mg 2؉ and Co(NH 3 ) 6 3؉ , in which the charge is centrally concentrated, yield lower P values than the polyamines putrescine 2؉ and spermidine 3؉ , in which the charge is linearly distributed. The elastic stretch modulus, S, and P display opposite trends with ionic strength, in contradiction to predictions of macroscopic elasticity theory. DNA is well described as a worm-like chain at concentrations of trivalent cations capable of inducing condensation, if condensation is prevented by keeping the molecule stretched. A retractile force appears in the presence of multivalent cations at molecular extensions that allow intramolecular contacts, suggesting condensation in stretched DNA occurs by a ''thermal ratchet'' mechanism.Ions strongly affect such biologically significant behavior of DNA as wrapping around nucleosomes, packaging inside bacteriophage capsids, and binding to proteins involved in transcriptional initiation and elongation. While such influence is often explained by relatively simple ion exchange equilibria (1, 2), in many cases ions appear to exert their effect by modifying the structure and mechanical properties of DNAits bending and torsional rigidity. The study of the ionic dependence of the elastic properties of DNA is therefore essential to understand the energetics of these key biological processes.Recent technical advances in nanomanipulation have allowed the mechanical behavior of single DNA molecules to be studied. Magnetic beads (3, 4), micro fibers (5), optical traps (6), and hydrodynamic flow (7) have been used to apply a wide range of forces to individual bacteriophage DNA molecules. Smith et al. (6) have recently described three regimes in the elastic response of -bacteriophage DNA ( DNA) molecules. Between 0.01 and 10 pN, the molecule behaves as an entropic spring and is well described by the worm-like chain (WLC) model (8-10), from which a persistence length, P, and a contour length, L o , can be obtained. Between 10 and 65 pN, the molecule deviates from the predictions of the inextensible WLC as it extends beyond its B-form contour length. From this ''enthalpic elasticity'' regime an elastic stretch modulus, S, can be obtained. Finally, at about 65 pN, the molecule suddenly yields in a highly cooperative fashion and overstretches Ϸ1....

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Section: Persistence Lengthsupporting

confidence: 88%

“…( ii) Molecules of different lengths can be studied in a variety of solution conditions at molecular extensions where excluded volume effects, which often complicate the interpretation of bulk experiments (ref. 22 and references therein), may be neglected. ( iii) DNA is condensed into compact particles by multivalent cations.…”

Section: Discussionmentioning

confidence: 99%

Ionic effects on the elasticity of single DNA molecules

Baumann

Smith

Bloomfield

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

923

111

996

View full text Add to dashboard Cite

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“…1 Many different methods have been used to determine the persistence length of defined-sequence DNA molecules. These methods include light scattering, 3,4 ligase-catalyzed cyclization, 5 flow dichroism, 6 cryoelectron microscopy, 7 scanning force microscopy, 8,9 force-measuring laser tweezers (FMLT), 10,11 transient electric birefringence (TEB), 12,13 and transient electric dichroism (TED). 14,15 The consensus value of the persistence length obtained for relatively short, well-characterized DNA molecules is ϳ 450 -500 Å, if the solution contains at least 100 M Mg 2ϩ or 10 mM Na ϩ ions.…”

Section: Introductionmentioning

confidence: 99%

DNA persistence length revisited

2002

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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.

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“…720 Å or decreases at high ionic strength (380 romolecule from a mammalian source and an aver-Å ; 3.0M). 15 DNA fragments on the order of a perage base pair molecular weight of 660 g/mol monosistence length have been determined to behave mer. However, any manipulations by the manufacas rigid rods.…”

Section: Introductionmentioning

confidence: 99%

The phase morphology and crystal growth habits of DNA fractions. Optical microscopy and light scattering

Monar

Phillips

1997

J. Polym. Sci. B Polym. Phys.

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Polydisperse DNA of reasonable molecular weights was prepared from a mammalian source via sonication and fractionation. A method for characterizing the molecular weight using gel electrophoresis is described. Quiescent crystallization was studied in thin films of one of the fractions induced by rapidly changing the hydration state isothermally. We report the occurrence of the semicrystalline nature of DNA. The crystal growth occurring via aggregates is best described as sheaves and spherulites from DNA gels in the relative humidity range (RH) corresponding to A‐DNA. These habits exhibit primary nucleation and secondary growth, which closely resemble those of melt‐crystallized, synthetic macromolecules and, in a follow‐up report, will be shown to be lamellar in nature. Small, needle‐like crystals are observed for B‐DNA hydration levels, and are unstable at lower hydration levels. A transformation from needle to lamellar crystals can occur, even when the primary nucleation of lamellar forms is otherwise absent at that hydration level, through a cylindrical phase exhibiting selective reflection of colored bands. The hydration level plays, in part, the role of the supercooling in this system and the long‐known hysteresis in the formation and dissolution of the A‐DNA (crystals) can now be viewed in light of those factors known to operate in semicrystalline systems. A morphological phase diagram is developed and is in accord with the known physical evidence. Because this preparation and these morphological observations are without precedence, substantial detail into methodology is included for this first article in the series. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 1843–1854, 1997

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Effects of Na⁺ on the persistence length and excluded volume of T7 bacteriophage DNA

Cited by 78 publications

References 40 publications

Ionic effects on the elasticity of single DNA molecules

Ionic effects on the elasticity of single DNA molecules

DNA persistence length revisited

The phase morphology and crystal growth habits of DNA fractions. Optical microscopy and light scattering

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Effects of Na+ on the persistence length and excluded volume of T7 bacteriophage DNA

Cited by 78 publications

References 40 publications

Ionic effects on the elasticity of single DNA molecules

Ionic effects on the elasticity of single DNA molecules

DNA persistence length revisited

The phase morphology and crystal growth habits of DNA fractions. Optical microscopy and light scattering

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Product

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Effects of Na⁺ on the persistence length and excluded volume of T7 bacteriophage DNA