The hydrodynamics of DNA electrophoretic stretch and relaxation in a polymer solution

Theories of DNA electrophoretic separations generally treat the DNA as a free draining polymer moving in an electric field at a rate that depends on the effective charge density of the molecule. Separations can occur in sieving media ranging from ultradilute polymer solutions to tightly cross-linked gels. It has recently been shown that DNA is not free-draining when both electric and nonelectric forces simultaneously act on the molecule, as occurs when DNA collides with a polymer during electrophoretic separations. Here we show that a semidilute polymer solution screens the hydrodynamic interaction that results from the application of these forces. Fluorescently labeled DNA tethered at one end in a semidilute solution of hydroxyl-ethyl cellulose stretch more in an electric field than they stretch in free solution, and approach free-draining behavior. The steady stretching behavior is predicted without adjustable parameters by a theory developed by Stigter using a hydrodynamic screening length found from effective medium theory. Data on the relaxation of stretched molecules after the electric field is removed agree with the Rouse model prediction, which neglects hydrodynamic interactions. The slowest relaxation time constant, tau(R), scales with chain length as tau(R) approximately L(1.9+/-0.17) when analyzed by the data collapse method, and as tau(R) approximately L(2.17+/-0.17) when analyzed by multiexponential fit.     

Elasticity theory of the B-DNA to S-DNA transition.

We propose in this note a simple model--the two-state Worm Like Chain--to describe the elasticity of the recently discovered stress-induced transformation from B-DNA to S-DNA. The model reduces for low tractions to the well-known Worm Like chain theory, which is used to describe the elastic properties of B-DNA, while in the limit of high chain-bending moduli it reduces to the two-state Ising model proposed by Cluzel et al. for the B-S transition [Cluzel, P., A. Lebrun, C. Heller, R. Lavery, J-L. Viovy, D. Chatenay, and F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794]. Our model can be treated analytically to produce an explicit form of the force-extension relationship which agrees reasonably with the observations. We use the model to show that conformational fluctuations of the chain play a role also for the B to S transformation.     

Free solution mobility of oligomeric DNA

The free solution electrophoretic mobility of a charged oligomer in an ionic solvent that approximately takes into account relaxation field effects, screening of the velocity field, and the hydrodynamic interactions resulting from motions of the charges due to an electric field is described. For double‐stranded DNA, the free solution electrophoretic mobility under ionic strengths determined by the buffer and pH conditions relevant to capillary electrophoresis increases with increasing molecular weight up to few hundred base pairs. © 1999 John Wiley & Sons, Inc. Biopoly 49: 209–214, 1999     

Electrokinetic stretching of tethered DNA

During electrophoretic separations of DNA in a sieving medium, DNA molecules stretch from a compact coil into elongated conformations when encountering an obstacle and relax back to a coil upon release from the obstacle. These stretching dynamics are thought to play an important role in the separation mechanism. In this article we describe a silicon microfabricated device to measure the stretching of tethered DNA in electric fields. Upon application of an electric field, electro-osmosis generates bulk fluid flow in the device, and a protocol for eliminating this flow by attaching a polymer brush to all silicon oxide surfaces is shown to be effective. Data on the steady stretching of DNA in constant electric fields is presented. The data corroborate the approximate theory of hydrodynamic equivalence, indicating that DNA is not free-draining in the presence of both electric and nonelectric forces. Finally, these data provide the first quantitative test of a Stigter and Bustamante's detailed theory of electrophoretic stretching of DNA without adjustable parameters. The agreement between theory and experiment is good.     

DNA persistence length revisited

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.     

Optimizing conditions for DNA isolation fromPinus radiata

Summary Genomic DNA was isolated fromin vitro Pinus radiata seedling with five DNA isolation protocols commonly used for pines. The methods described by Jobes et al. (1995) and Nelson et al. (1994) utilize sodium dodecyl sulfate, whereas those of Murray and Thompson (1980), Doyle and Doyle (1990), and Devey et al. (1996) use cetyltrimethyl ammonium bromide for cell lysis. The quality and quantity of the isolated DNA was measured and compared. Lithium chloride was found to be more effective than RNase for minimizing the amount of RNA present in the solution. Protocols described by Jobes et al. (1995) and Devey et al. (1996) yielded a large quantity of pure DNA which was suitable for restriction enzyme digestion and polymerase chain reaction amplification. With these methods, 37 to 79 μg of DNA with an A_260/280 ratio between 1.7 and 1.9 was obtained from 1 g ofPinus radiata seedlings grownin vitro.     

Shielding effects of small ions in gel electrophoresis of DNA

Results of free electrophoresis and free sedimentation of charged rods are introduced to allow for electrical double-layer effects in the gel electrophoresis of DNA, modeled as a random flight sequence of rodlike Kuhn chain elements. The kinetics of DNA is shown to depend strongly on the orientation of the chain elements with respect to the external field and with respect to the direction of their velocity. The new theory gives approximate agreement between the DNA charge derived from electrophoresis of free and tethered DNA (close to 1.0e per DNA phosphate in both cases), compared with the earlier discrepancy of a factor 10 or 20 for the theory without shielding by salt. As part of a realistic force field for macromolecular dynamics simulation, the small ion effects are included in an expression for the gel forces restraining the DNA in gel electrophoresis from moving as in free electrophoresis.     

The purple bacterial photosynthetic unit

Now is a very exciting time for researchers in the area of the primary reactions of purple bacterial photosynthesis. Detailed structural information is now available for not only the reaction center (Lancaster et al. 1995, in: Blankenship RE et al. (eds) Anoxygenic Photosynthetic Bacteria, pp 503–526), but also LH2 from Rhodopseudomonas acidophila (McDermott et al. 1995, Nature 374: 517–521) and LH1 from Rhodospirillum rubrum (Karrasch et al. 1995. EMBO J 14: 631–638). These structures can now be integrated to produce models of the complete photosynthetic unit (PSU) (Papiz et al., 1996, Trends Plant Sci, in press), which opens the door to a much more detailed understanding of the energy transfer events occurring within the PSU.Abbreviations Bchl bacteriochlorophyll - LH light-harvesting - PSU photosynthetic unit Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences     

Pollen Tubes: a Model System for Plant Cell Growth*

Recent observations of pollen tubes show that these tubes may grow in a pulsatory fashion (Pierson et al., 1995; Plyushch et al., 1995; Li et al., 1996; Geitmann et al., 1996a, 1996b), in which phases of fast and slow growth alternate regularly. The occurrence of pulsatory growth has been used by Geitmann and coworkers (1996b) to study factors that might control growth. Their results emphasize the role of the cell wall and secretory events in regulating pollen tube growth. Here we will briefly review recent results related to the role of exocytosis, cytoskeleton, calcium and the cell wall in pollen tube growth.     

Dynamic bending rigidity of DNA

Rapidly relaxing components in the decay of the transient electric dichroism of DNA restriction fragments were reported by Diekmann et al. [(1982) Biophys. Chem. 15, 263-270] and P?rschke et al. [(1987) Biopolymers 26, 1971-1974]. These are analyzed using a new normal mode theory for weakly bending rods and assigned to bending. The longest bending relaxation times for fragments with 95-250 base pairs coincide with the theoretical curve calculated for a dynamic bending rigidity corresponding to a dynamic persistence length Pd = 2100 A. Analysis of the relative amplitudes of fast and slow components following weak orienting pulses is also consistent with a rather large dynamic persistence length. The enhancement of the relative amplitude of the fast component in large electric fields is attributed to steady-state bending of initially perpendicular DNAs by the field. Several reasons are proposed why the dynamic bending rigidity is 4 times larger than the apparent static bending rigidity inferred from equilibrium persistence length measurements on the same fragments.     

Human immunodeficiency virus drug therapy and virus load.

Analysis of the short-term dynamics of human immunodeficiency virus (HIV) type 1 infection in response to drug therapy has elucidated crucial kinetic properties of viral dynamics in vivo (D. D. Ho et al., Nature 373:123-126, 1995; A. S. Perelson et al., Science 271:1582-1586, 1996; X. Wei et al., Nature 373:117-122, 1995). Here we investigated long-term changes in virus load in patients treated with a combination of lamivudine and zidovudine to identify principal factors responsible for the observed 10- to 100-fold sustained suppression of virus load in vivo. Interestingly, most standard accounts of virus dynamics cannot explain a large sustained reduction without shifting the virus very close to extinction. The effect can be explained by taking into consideration either (i) the immune response against HIV, (ii) the killing of uninfected CD4 cells, or (iii) the differential efficacies of the drugs in different cell populations.     

Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations

Hydrodynamic properties of small single-stranded RNA homopolymers with three and six nucleotides in free solution are determined from molecular dynamics simulations in explicit solvent. We find that the electrophoretic mobility increases with increasing RNA length, consistent with experiment. Diffusion coefficients of RNA, corrected for finite-size effects and solvent viscosity, agree well with those estimated from experiments and hydrodynamic calculations. The diffusion coefficients and electrophoretic mobilities satisfy a Nernst-Einstein relation in which the effective charge of RNA is reduced by the charge of transiently bound counterions. Fluctuations in the counterion atmosphere are shown to enhance the diffusive spread of RNA molecules drifting along the direction of the external electric field. As a consequence, apparent diffusion coefficients measured by capillary zone electrophoresis can be significantly larger than the actual values at certain experimental conditions.     

Re-evaluation of phytohormone-independent division of tobacco protoplast-derived cells

We have used a [³H] thymidine incorporation assay and microscopic observation in order to reassess recently published data dealing with the response of tobacco protoplasts to phytohormones, lipochitooligosaccharides and peptides ( Harling et al . 1997 ; Hayashi et al . 1992 ; Miklashevichs et al . 1996 ; Miklashevichs et al . 1997 ; Röhrig et al . 1995 ; Röhrig et al . 1996 ; van de Sande et al . 1996 ; Walden et al . 1994 ). These proliferation assays reveal that, in contrast to published data, isolated cells of the investigated mutant plant lines axi159 ( Hayashi et al . 1992 ; Walden et al . 1994 ), axi4/1 ( Harling et al . 1997 ) and cyi1 ( Miklashevichs et al . 1997 ), which were generated by activation T-DNA tagging, were unable to grow in the absence of auxin or cytokinin. Furthermore, lipochitooligosaccharides which play a key role in the induction of nodules on roots of legumes were unable to promote auxin- or cytokinin-independent cell division in tobacco protoplasts as claimed by Röhrig et al . (1995 , 1996 ). The finding of van de Sande et al . (1996 ) that ENOD40 confers tolerance of high auxin concentration to wild-type tobacco protoplasts was also reinvestigated. The results of our investigations show that we were unable to reproduce the proliferation data presented in this study, which were obtained by counting tobacco protoplast-derived cells undergoing division. In total, none of the published data on phytohormone-independent division of tobacco cells could be reproduced.     

The activity of abdominal stretch receptors during non-giant swimming in the crayfish<Emphasis Type="Italic"> Cherax destructor</Emphasis> and their role in hydrodynamic efficiency

Recordings were made from the nerve innervating the stretch receptors of the abdominal muscle receptor organs and slow extensor muscles of tethered crayfish, Cherax destructor, during so-called non-giant swimming. The stretch receptors were active during the flexor phase of swimming but the duration and pattern of activity varied from cycle to cycle. Their pattern of firing was modified by the activity of the large accessory neurons which make direct inhibitory synapses upon them. Neither the stretch receptors nor the accessory neurons were active during the extensor phase of the cycle. The timing and extent of tailfan movements during the period of stretch receptor activity were measured from video records before and after the stretch receptor nerves were cut in the second to fifth segments. The promotion of the tailfan during flexion was significantly delayed and the minimum angle to which the uropods were remoted at the end of flexion significantly larger in denervated animals. We propose that afferent information from the stretch receptors coordinates the timing and extent of tailfan movements according to variations in the positioning and movement of the abdominal segments such that the hydrodynamic efficiency of the tailfan is enhanced on a cycle by cycle basis during non-giant swimming.Abbreviations A# abdominal segment number - Acc accessory neuron - LUU large unidentified unit - MRO muscle receptor organ - NGS non-giant swimming - SEMN slow extensor motor neuron - SR stretch receptor neuron     

An efficient conformational sampling method for homology modeling

The structural refinement of protein models is a challenging problem in protein structure prediction (Moult et al., Proteins 2003;53(Suppl 6):334-339). Most attempts to refine comparative models lead to degradation rather than improvement in model quality, so most current comparative modeling procedures omit the refinement step. However, it has been shown that even in the absence of alignment errors and using optimal templates, methods based on a single template have intrinsic limitations, and that refinement is needed to improve model accuracy. It is thought that failure of current methods originates on one hand from the inaccuracy of the effective free energy functions adopted, which do not represent properly the energetic balance in the native state, and on the other hand from the difficulty to sample the high dimensional and rugged free energy landscape of protein folding, in the search for the global minimum. Here, we address this second issue. We define the evolutionary and vibrational armonics subspace (EVA), a reduced sampling subspace that consists of a combination of evolutionarily favored directions, defined by the principal components of the structural variation within a homologous family, plus topologically favored directions, derived from the low frequency normal modes of the vibrational dynamics, up to 50 dimensions. This subspace is accurate enough so that the cores of most proteins can be represented within 1 A accuracy, and reduced enough so that Replica Exchange Monte Carlo (Hukushima and Nemoto, J Phys Soc Jpn 1996;65:1604-1608; Hukushima et al., Int J Mod Phys C: Phys Comput 1996;7:337-344; Mitsutake et al., J Chem Phys 2003;118:6664-6675; Mitsutake et al., J Chem Phys 2003;118:6676-6688) (REMC) can be applied. REMC is one of the best sampling methods currently available, but its applicability is restricted to spaces of small dimensionality. We show that the combination of the EVA subspace and REMC can essentially solve the optimization problem for backbone atoms in the reduced sampling subspace, even for rather rugged free energy landscapes. Applications and limitations of this methodology are finally discussed.     

Direct observation of the self-association of dilute proteins in the presence of inert macromolecules at high concentration via tracer sedimentation equilibrium: theory, experiment, and biological significance.

The technique of tracer sedimentation equilibrium [Rivas, G., et al. (1994) Biochemistry, 2341-2348 (1); Rivas, G., et al. (1996) J. Mol. Recognit. 9, 31-38 (2)] is utilized, together with an extension of the theory of sedimentation equilibrium of highly nonideal solutions [Chatelier and Minton, (1987) Biopolymers 26, 1097-1113 (3)], to characterize the thermodynamic activity and/or the state of association of a dilute, labeled macromolecular solute in the presence of an arbitary concentration of a second, unlabeled macromolecular solute. Experiments are performed on solutions of labeled fibrinogen (0.25-1 g/L) in bovine serum albumin (0-100 g/L) in the presence and absence of divalent cations (Ca(2+), Mg(2+)), and on solutions of labeled tubulin (0.2-0.6 g/L) in dextran (0-100 g/L). It is found that in the absence of the divalent cations, the large dependence of the thermodynamic activity of fibrinogen on BSA concentration is well accounted for by a simple model for steric repulsion. In the presence of the cations and sufficiently large concentrations of BSA (>30 g/L), fibrinogen appears to self-associate to a weight-average molar mass approximately twice that of monomeric fibrinogen. Tubulin appears to self-associate to an extent that increases monotonically with increasing dextran concentration, reaching a weight-average molar mass almost 3 times that of the alphabeta dimer in the presence of 100 g/L dextran. Possible biological ramifications are discussed.     

20-hydroxyeicosatetraenoic acid (20-HETE): structural determinants for renal vasoconstriction

The effects of natural and synthetic eicosanoids on the diameter of rat interlobular arteries studied in vitro were compared to that of the potent, endogenous vasoconstrictor 20-HETE. Vasoconstrictor activity was optimum for chain lengths of 20-22 carbons with at least one olefin or epoxide between located between C(13)-C(15) and an oxygen substituent at C(20)-C(22). The presence of delta (Zou et al. Am. J. Physiol. 1996, 270, R228; Gebremedhin, D. et al. Am. J. Physiol. 1998, 507, 771)-, delta (Carroll et al. Am. J. Physiol. 1996, 271, R863; Vazquez et al. Life Sci. 1995, 56, 1455)-, or delta (Imig et al. Hypertension 2000, 35, 307; Lopez et al. Amer. J. Physiol. 2001, 281, F420)-olefins had no influence on the vasoconstrictor response whereas the introduction of a C(7)-thiomethylene enhanced potency. A sulfonamide or alcohol, but not a lactone, could replace the C(1)-carboxylate. These data were used to construct a putative binding domain map of the 20-HETE receptor consisting of: (i) a comparatively open, hydrophilic binding site accommodating the C(1)-functionality; (ii) a hydrophobic trough spanning the olefins; (iii) a shallow pocket containing a critical pi-pi binding site in the vicinity of the pi (Ito et al. Am. J. Physiol. 1998, 274, F395; Quigley, R.; Baum, M.; Reddy, K. M.; Griener, J. C.; Falck, J. R. Am. J. Physiol. 2000, 278, F949)-olefin; and (iv) an oxyphilic binding site proximate to the omega-terminus.     

Molecular dynamics simulations of beta-turn forming tetra- and hexapeptides

It was previously shown that the structural ensemble of model peptides DDKG and GKDG (H. Ishii et al. Biopolymers 24, 2045-2056, 1985), DEKS (A. Otter et al. J. Biomol. Struct. Dyn. 7, 455-476, 1989) NPGQ (F. R. Carbone et al. Int. J. Pept. Protein. Res. 26, 498-508, 1985), SALN (H. Santa et al. J. Biomol. Struct. Dyn. 16, 1033-1041, 1999), SYPFDV and SYPYDV (J. Yao et al. J. Mol. Biol. 243, 736-753, 1994), VP(D)AH and VP(D)SH (B. Imperiali et al. J. Am. Chem. Soc. 114, 3182-3188, 1992) in solution contains a significant - or in some cases dominant - proportion of beta-turn conformation. In this study, a protein database was searched for the above, unprotected sequences which incorporate only L-amino acid residues. Simulated annealing and 25 ns MD simulations of structures were also performed. The DSSP and STRIDE secondary structure-assigning algorithms and clustering were used to analyze trajectories and i, i+3 hydrogen bonds were also sought. The DSSP analysis showed a fluctuation between beta-turn and random meander structure, although bend structures were not detected because of the insufficient length of peptide chains. This alternating trend was confirmed when the STRIDE algorithm was used to analyze trajectories, but STRIDE assigned more turn structures. The population of the strongest clusters was above 40% and the middle structures adopted beta-turn structure for most sequences. These results are in good agreement with previous experimental results and support the idea of the ultra-marginal stability of turns in the absence of stabilizing long-range interactions of the neighboring segments of a polypeptide chain. However, interactions between the side-chains in tetrapeptides could also contribute to turn stability and result in unusual stability in some cases. Our observations suggest that such interactions are the consequence rather than the driving force of turn formation.     

The response of DNA length and twist to changes in ionic strength

We examine twist‐stretch coupling of unconstrained DNA using polyelectrolyte theory as applied to a line‐charge model along with published data on the ionic‐strength dependence of the twist angle. We conclude that twist‐stretch coupling is negative: environmental changes that stretch free DNA, unconstrained by externally applied pulling or twisting forces, are accompanied by unwinding of the double helix. We also analyze a helical model and conclude that the observed unwinding of the DNA helix when ionic strength is decreased is driven by radial swelling of the helix. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 223–226, 2015.