Quasielastic light scattering by biopolymers. IV. Tertiary collapse of calf thymus DNA in 5.5M LiCl

Circular dichroism has been commonly employed to infer the conformation of DNA in solution. The basis of the conformational assignments is the work of Tunis-Schneider and Maestre, wherein CD spectra of DNA were obtained under conditions comparable to those employed in the x-ray diffraction studies of A-, B-, and C-DNA. It has recently been suggested that the CD spectrum of DNA in chromatin, which is similar to the CD spectrum of the C-form DNA, is a superposition of the normal B-DNA spectrum and a single negative band, centered at 275 nm. This negative band is qualitatively identical to the spectrum for condensed Ψ-form DNA. We have employed the hydrodynamic methods of quasielastic light scattering and sedimentation velocity to determine the extent of DNA tertiary structural alteration in 5.5M LiCl as a possible explanation of the C-form CD spectrum. These studies suggest an eightfold contraction of the Stokes hydrodynamic volume for calf thymus DNA in going from 0.4M NH₄Ac to 5.5M LiCl, with no change in molecular weight. The estimated maximum presistence length of DNA in 5.5M LiCl is estimated to be 20.0 nm compared to the “minimum” value of 44.7 nm in NaCl solutions. The value 20.0 nm corresponds to a maximum radius of 16.7 nm for a “continuously coiled” cylinder of DNA, which compares with the value 5.0 nm of DNA in the nucleosome unit of chromatin.     

Texture formation in DNA films with alkali metal chlorides

The formation of textures in DNA films with LiCl, NaCl, KCl, RbCl, and CsCl salts has been studied. The films are prepared by evaporation of water solution with highly polymerized calf thymus DNA and excess salt of specific type. For DNA solution with 10 mM concentration of NaCl, KCl, and RbCl the films with dendritic textures have been obtained, whereas in case of CsCl the textures in the films appear only at 30 mM concentration of excess salt in the initial solution. In the solution with LiCl, the textures in DNA films have not been observed within the whole range of concentration of excess salt under consideration. The analysis of parameters of DNA films with different salts has showed that evaporation of solution leads to crystallization of salt ions on DNA macromolecule and formation of DNA‐salt complexes. Electrostatic energy of the system of crystalline ordered ions and charges of DNA chains has been estimated to study the stability of DNA‐salt complexes. The results obtained for different salts have been showed that the presence of DNA macromolecule enhances crystallization as compared with solution without DNA. The property of excess salt to form the crystalline structures has been found to decrease in the following order: KCl > NaCl > RbCl > CsCl > LiCl. The results of estimation are in good agreement with the experimentally observed dependence of texture formation on excess salt type. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 508–516, 2013.     

Conformational characteristics of deoxyribonucleic acid-butylamine complexes with C-type circular dichroism spectra. 2. A Raman spectroscopic study

The derivatives of calf thymus DNA in which n-butylamine is covalently attached as described in the preceding paper in this series [Chen, C. Y., Pheiffer, B. H., Zimmerman, S. B., & Hanlon, S. (1983) Biochemistry (preceding paper in this issue)] were examined by Raman spectroscopy. As previously mentioned, these complexes exhibit profoundly decreased rotational strengths of the positive band of the circular dichroism (CD) spectrum above 260 nm, with the most heavily substituted (ca. 0.12 mol of amine/mol of nucleotide) resembling that of DNA in 11 m LiCl. Raman spectra of all complexes and their controls in the form of either fibers at 98% relative humidity or gels at 40 mg/mL in 20 mM NaCl, pH 7, show typical B-type spectra with no evidence of significant amounts of C, A, Z, or disordered forms. We have thus concluded that the assignment of the nonconservative CD spectrum of DNA typically observed in concentrated electrolyte solutions to a C form is in error. Both these Raman data and the X-ray results reported in the previous paper indicate that the structure giving rise to the C CD spectrum has B-form backbone geometry.     

Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration.

The data and approach reported in paper I (Hanlon et al., 1975, preceding paper) have been used to calculate the fractional changes in secondary structure of calf thymus deoxyribonucleic acid which occur in aqueous solutions as a function of the concentration of NaCl, KCl, LiCl, CsCl, and NH4Cl. There is a continuous loss in the "B" character of the nucleic acid with concomitant production of the C and, in some instances, an A form, as well, as the salt concentration increases. Sedimentation velocity studies suggest that there is an accompanying change in the hydrodynamic characteristics of the DNA molecules, as well. Utilizing the existing hydration data in the literature (Hearst and Vinograd, 1961a,b; Hearst, 1965; Tunis and Hearst, 1968a; Cohen and Eisenberg, 1968; Falk et al., 1962, 1963a,b), we have found that a gradual loss of "B" character and a decrease in the frictional coefficient of DNA occur as the net hydration of DNA is reduced from the fully hydrated from (60-80 mol of H2O/mol of nucleotide) to values of ca. 12-14 mol of H2O/mol of nucleotide. Below that value, a more precipitous decrease in these properties occurs. Extrapolation of the linear relationship observed between the fractional B content and the net hydration in the latter regions yield values of ca. 18 mol of H2O/mol of nucleotide at 100% B and ca. 4 mol of H2O/mol of nucleotide at 0% B (i.e., 100% C or C + A) for the alkali metal salts of DNA. The ammonium salt retains somewhat more H2O in the C and A forms (ca. 7). These results together with the hydration site assignments of Falk et al. (1962, 1963a,b) are interpreted in terms of a hydration model for DNA in aqueous solution in which an intact primary hydration shell of ca. 18 mol of H2O/mol of nucleotide is required for the maintenance of the "B" conformation. Removal of all but those water molecules solvating the phosphate groups results in the conversion to the C forms, predominantly, with a small amount of A structure formed as well in some salts. The accompanying changes in the sedimentation coefficients suggest that the DNA molecule assumes a more compact and/or flexible form under these conditions in which it is mainly in the C and A structures. The combination of these two events which ensue upon dehydration create a polymeric structure which can be more easily packaged in biological systems.     

Cation radius effects on cell-free translation in rabbit reticulocyte lysate

The effect of monovalent cation concentrations on the translation was examined in the rabbit reticulocyte cell-free system. The translation of standard reporter gene luciferase was studied using different concentrations of LiCl, NaCl, KCl, RbCl, CsCl, NH(4)Cl, and (CH(3))(4)NCl and the acetates of Na(+), K(+), and NH4(+). Only the salts of K(+), Rb(+), and NH4(+) and to some minor extent of Cs(+) significantly supported translation. Optimum concentrations were dependent on the cation used. Optimum concentrations ranged between 40 mM (NH(4)Ac), 80 mM (KCl, NH(4)Cl), and 100 mM (RbCl, KAc). The maximum efficiency of translation depends on the ionic radius of the cation used. KCl and RbCl were superior to all other salts tested in stimulating in vitro translation. The results were confirmed, using a second reporter system, M-hirudin. Here, however, broad optima were observed with RbCl being slightly superior to KCl in supporting translation.     

Activation of dynein adenosine triphosphatase and flagellar motility of demembranated spermatozoa by monovalent salts at 40 degrees C in the domestic fowl, Gallus domesticus

1. At 40 degrees C, around the normal avian body temperature, demembranated fowl spermatozoa with no addition of monovalent chlorides were immotile. 2. Demembranated spermatozoa become motile at 40 degrees C when 0.1-0.5 M concentrations of NH4Cl, NaCl and KCl were added to the reactivation medium, with maximum motility occurring at 0.2-0.3 M in all cases. 3. The addition of NH4Cl, NaCl and KCl also stimulated the ATPase activity of crude dynein extract. In contrast, LiCl did not appreciably affect motility and ATPase activity. 4. These results showed that the flagellar dynein ATPase activity of fowl spermatozoa could be stimulated by the addition of certain monovalent chlorides, except LiCl, and demembranated spermatozoa might be motile at 40 degrees C.     

Differentiation and characterization of the cytoplasmic and nuclear deoxyribonucleic acid polymerases from baby hamster kidney cells.

Distinct DNA polymerase activities have been found in the cytoplasmic and nuclear fractions of a baby hamster kidney cell line. They were separated by chromatography on DEAE-cellulose and partially purified by ammonium sulfate fractionation, DNA - cellulose and linear sucrose gradients. The cytoplasmic DNA polymerase exhibited an S-coefficient of 6.95 S in 0.15 M NaCl and its activity was highly sensitive to inhibition by N-ethylmaleimide and elevated temperatures, regardless of the presence of DNA template or other cofactors. It was stimulated by monovalent salts in the order of NH4 Cl greater than KCl greater than NaCl greater than CsCl greater than LiCl (inhibitory). The DNA polymerase extracted from nuclei sedimented with an S-value of 3.47 S, was resistant to inactivation by N-ethylmaleimide, and maximally stimulated by NaCl, while also being inhibited by LiCl. For optimal activity, both DNA polymerase activities required a divalent cation, with MgCl2 being more effective than MnCl2. Although the optimal pH values for the two enzyme activities differed slightly, glycine - NaOH buffer induced an alkaline shift of 1.5 pH units in the optimum of both enzymes. This was accompanied by an increase in the effectiveness of MnCl2 relative to MgCl2 for the cytoplasmic DNA polymerase.     

Lithium fluxes in Paramecium and their relationship to chemoresponse.

Paramecia respond to environmental stimuli by altering swimming behavior to disperse from or accumulate in the vicinity of the stimulus. We have found, using the T-maze assay, that treatment of paramecia with LiCl in a time- and concentration-dependent manner modifies the normal response to folate, acetate, and lactate from attraction to no response or even repulsion. Responses to NH4Cl were unaffected and to cAMP were variably affected by LiCl. Cells incubated in the presence of K+, or both Na+ and K+, but not Na+ alone reliably recovered attraction to folate. Treatment of cells with 4 mM LiCl for 1 h dramatically slowed swimming speed from about 1 mm/s in NaCl or KCl (control) to 0.18 mm/s in LiCl. Li-treated cells subsequently incubated in 4 mM NaCl, KCl or sequentially in KCl and NaCl for a total of 20 min increased their swimming speed to 0.35, 0.45 and 0.67 mm/s, respectively. Paramecia readily took up Li+ in Na(+)- and K(+)-free media reaching intracellular concentrations of 5-10 mM in 10 mM extracellular Li+. Efflux of intracellular Li+ was stimulated 35% by extracellular 10 mM NaCl and 185% by 10 mM KCl over 10 mM choline chloride. Incubation of cells in 10 mM LiCl for 1 h inhibited the rate of Ca2+ efflux by 44% compared to cells in 10 mM NaCl. This may relate to the mechanism by which Li+ perturbs chemoresponse. A mutant with defects in Ca homeostasis responds normally to NH4Cl, but not to any of the stimuli that are affected by LiCl.     

Structure of phenylalanine-accepting transfer ribonucleic acid and of its environment in aqueous solvents with different salts

Yeast tRNA(Phe) was studied in different salt-containing solvents by UV absorbance and small-angle neutron scattering (SANS). This extends results obtained previously in NaCl and KCl solutions [Li, Z.-Q., Giegé, R., Jacrot, B., Oberthür, R., Thierry, J. C., & Zaccai, G. (1983) Biochemistry 22, 4380-4388]. As expected, at low concentrations of all salts studied, the tRNA molecule is unfolded. The importance of specific counterion interactions and the flexibility of the macromolecule are emphasized by the observation that it cannot take up its folded structure in N(CH3)4Cl solvents, even when that salt concentration is increased to 1 M, in the absence of Mg ions. In CsCl solvents, on the other hand, the folded conformation is obtained in salt concentrations above about 0.2 M, similar to NaCl or KCl. By a comparison of SANS results in CsCl H2O and CsCl 2H2O solvents with the data from NaCl and KCl solvents, thermodynamic and structural parameters were derived for the solvated macromolecule. All the data are accounted for, quantitatively, by a model for the particle in NaCl, KCl, or CsCl solution made up of tRNA76-, closely associated with 76 positive hydrated counterions, surrounded by an aqueous solvent layer that excludes salt (and, therefore, of density different from that of bulk solvent). The mass of water in that layer depends on salt concentration, and the values found are consistent with those predicted by the Donnan effect.     

Developmental changes in sugar responses of the chorda tympani nerve in preweanling rats

To clarify developmental changes in the gustatory system of the rat, integrated taste responses from the chorda tympani (CT) nerve were recorded and analyzed at different postnatal ages. The response magnitude was calculated relative to the response to the standard, 0.1 M NH4Cl. Even at 1 week of age, the CT responded well to all tested 0.1 M chloride salts (NH4Cl, NaCl, LiCl, KCl, RbCl and CsCl). The responses to 0.1 M NaCl and LiCl increased with increasing age of the rat while response magnitudes to KCl, RbCl and CsCl did not change up to 8 weeks. At 1 week, the integrated response pattern was quite similar to that in adult rats for NaCl, HCl and quinine hydrochloride (QHCl). The concentration-response functions for NaCl, HCl, QHCl and sucrose at 2 weeks were essentially the same as those at 8 weeks. These results suggest that taste buds in the 2-week-old rat are functionally mature for the detection of the four basic taste stimuli. The relative magnitude of the responses to the various sugars was smaller at 1 week compared to the adult rat and reached a maximum at weeks 3-4, then decreased gradually with age. Among the six sugars, sucrose was the most effective followed by lactose. From weeks 1-4, the magnitude of the integrated taste response to fructose was smaller than that to lactose except at 3 weeks of age. Maltose, galactose and glucose were less potent stimuli than the other sugars tested. The response magnitude to lactose at 4 weeks had decreased compared to that for the other sugars. Taste responses to the sugars in preweanling and adult rats were not cross-adapted by the individual sugars. These results suggest that after 1 week of age during postnatal development in the rat, taste information from the CT rapidly increases in its importance for feeding behavior.     

Crystallization of phosphatidylserine bilayers induced by lithium

Utilizing differential scanning calorimetry and x-ray diffraction, 1,2-dimyristoyl-L-glycero-3-phospho-L-serine (DMPS) was shown to form hydrated bilayer membrane structures exhibiting a gel leads to liquid crystalline transition at 39 degrees C (delta H = 7.2 kcal/mol). Addition of up to molar concentrations of the alkali halides NaCl, KCl, Rl Cl, and CsCl produced relatively minor changes in DMPS bilayer structure or stability. For example, in the presence of 0.5 M NaCl, the transition temperature (Tc = 42 degrees C) and transition enthalpy (delta H = 7.0 kcal/mol) show only minor changes. In marked contrast, addition of LiCl results in "'crystallization" of the DMPS bilayer membrane structure. At 0.5 M LiCl, the crystalline DMPS exhibits a bilayer gel leads to liquid crystal transition at 89 degrees C accompanied by a high enthalpy change, delta H = 16.0 kcal/mol. Thus, Li+ induces an isothermal crystallization of DMPS bilayers, the hydrocarbon chains adopting a more ordered packing mode than the "hexagonal" arrangement of the gel state. In view of the widespread use of lithium in the treatment of manic-depressive illness, we also raise the possibility that interaction of Li+ with anionic membrane phospholipids could play a role in its pharmacological action.     

Structural transitions of calf thymus DNA in concentrated LiCl solutions

The solubility, sedimentation, circular dichroism, and absorption spectral characteristics of calf thymus DNA have been examined in concentrated solutions of LiCl (6-13 m) at 25 to 27 degree C. At all concentrations of LiCl, the DNA is base stacked and exhibits normal hypochromicty, At the upper end of this range of LiCl concentrations, DNA aggregates and ultimately precipitates completely from solution between 13 and 14 m LiCl. This aggregation process is dependent on concentration, base composition, and molecular weight of DNA. The sedimentation velocity data taken together with the absorbance spectral data suggest that the aggregation process leading to the formaiton of large structures beings at approximately equal to 9 m. Prior to the onset of aggregation, the circular dichroism (CD) spectra can be adequately fitted by a linear combination of contributions of the B, C, and A forms of DNA (Hanlon, S., Brudno, S., Wu, T. T., and Wolf, B. (1975), Biochemistry 14, 1648). Above 9 m LiCl, both factor analysis and a primitive version of matrix rank order analysis indicate that at least one additional spectral component is required to account for the observed CD spectra above 260 nm. The general shape of this additional component or distortion resembles the psi form of DNA.     

Salt specificity of a reduced nicotinamide adenine dinucleotide oxidase prepared from a halophilic bacterium

Extracts prepared from a halophilic bacterium contained a reduced nicotinamide adenine dinucleotide (NADH(2)) oxidase active at high solute concentrations. The cation requirement was nonspecific, since KCl, RbCl, and CsCl replaced NaCl with little or no loss of activity, and NH(4)Cl was only partially effective. Only LiCl failed to replace NaCl. No specific chloride requirement was observed although not all anions replaced chloride. Bromide, nitrate, and iodide were essentially ineffective, whereas acetate, formate, citrate, and sulfate proved suitable. The presence of sulfate affected the ability of a cation to satisfy the solute requirement. Sulfate enhanced the rate of NADH(2) oxidation when compared with the rate observed in the presence of chloride. Cations which were inactive as chlorides (LiCl and MgCl(2) at high concentrations) satisfied the cation requirement when added as sulfate salts. Although magnesium satisfied the cation requirement, a concentration effect, as well as an anion effect, was observed. In the presence of MgCl(2), little NADH(2) oxidation was observed at concentrations greater than 1 m. At lower concentrations, the rate of oxidation increased, reaching a maximal value at 0.1 m and remaining constant up to a concentration of 0.05 m MgCl(2). Magnesium acetate and MgSO(4) also replaced NaCl, and the maximal rate of oxidation occurred at 0.05 m with respect to magnesium. There was no change in the rate of oxidation at high magnesium acetate concentrations, whereas the rate of NADH(2) oxidation increased at higher concentrations of MgSO(4).     

Purification and amino-terminal amino acid sequence of an apurinic/apyrimidinic endonuclease from calf thymus.

An apurinic/apyrimidinic (AP) endonuclease (E.C.3.1.25.2) has been purified 1100 fold to apparent homogeneity from calf thymus by a series of ion exchange, gel filtration and hydrophobic interaction chromatographies. The purified AP endonuclease is a monomeric protein with an apparent molecular weight on SDS-PAGE of 37,000. On gel filtration the protein behaves as a protein of apparent molecular weight 40,000. DNA cleavage by this AP endonuclease is dependent on the presence of AP sites in the DNA. DNA cleavage requires the divalent cation Mg2+ and has a broad pH optimum of 7.5-9.0. Maximal rates of catalysis occur at NaCl or KCl concentrations of 25-50 mM. The amino acid composition and the amino-terminal amino acid sequence for this AP endonuclease are presented. Comparison of the properties of this AP endonuclease purified from calf thymus with the reported properties of the human AP endonuclease purified from HeLa cells or placenta indicate that the properties of such an AP endonuclease are highly conserved in these two mammalian species.     

Circular dichroism studies of salt- and alcohol- induced conformational changes in cyanophage S-2L DNA which contains amino 2 adenine instead of adenine.

DNA molecules containing AT pairs exhibit cesium cation specific conformational behavior. This specificity is shown to be cancelled with the title DNA, which not only concerns its conformational alterations in high-salt aqueous solutions but also the B-to-A transition induced by ethanol. S-2L DNA easily adopts the A-conformation in the presence of millimolar concentrations of CsCl which completely destabilize the A-conformation in calf thymus DNA. The present results demonstrate that the specific effects of cesium cations on DNA are connected with their binding to the AT pairs in the DNA minor groove.     

Effect of salts and organic solvents on the activity of Halobacterium cutirubrum catalase

Catalase in extracts of the extreme halophile Halobacterium cutirubrum exhibits up to threefold stimulation by 0.5 to 1.5 m monovalent salts and by 0.1 m divalent salts. Above these concentrations, inhibition of enzyme activity is observed. The inhibitory effect, and to some extent the stimulation, is salt-specific; the effectiveness of a salt in inhibiting enzyme activity depends on both cation and anion. Thus, the order of effectiveness is MgCl(2) > LiCl > NaCl > KCl > NH(4)Cl, and LiCl > LiNO(3) > Li(2)SO(4). The magnitude of enzyme inhibition for the salts tested is positively correlated with their molar vapor pressure depression in aqueous solution. Stimulation of enzyme activity was observed when one salt was added at its optimal concentration in the presence of inhibiting concentrations of another salt, indicating that the effect on the enzyme is not due to changing water activity but probably to enzyme-salt interaction. Aqueous solutions of ethylene glycol, glycerol, and dimethyl sulfoxide containing no ions influence enzyme activity in the same manner as do salts.     

Influence of Electrolytes on the Thicknesses of the Phospholipid Bilayers of Lamellar Lecithin Mesophases

Over a wide range of water contents, aqueous lecithin-water mixtures are mesophases in which lecithin bilayers alternate with water layers. This paper reports on low-angle X-ray diffraction measurements of the effects of electrolytes, at 1.0 N concentration, on the thicknesses of the bilayers in mesophases formed by the synthetic lecithin: 1-octadec-9-enyl-2-hexadecylglycerophosphocholine. With solutions of LiCl, NaCl, Na₂SO₄, KCl, and CsCl, the bilayer thicknesses are less than with pure water. The maximum reduction in bilayer thickness with these electrolytes is about 10% and occurs with mesophases of high content of KCl and CsCl solutions. With HCl solutions the bilayer thicknesses are about 5% greater than with pure water, and with CaCl₂ solutions the bilayer thicknesses are about the same as with pure water. The maximum amount of solution which can be mixed with lecithin before a second, purely aqueous phase is formed is also affected by electrolytes, the order for the various 1.0 N solutions being CsCl = KCl > NaCl > Na₂SO₄ > (pure water) = LiCl > CaCl₂.     

Form of DNA and the nature of interactions with proteins in chromatin.

Studies of native chromatins and of isolated nucleosomes (from calf thymus) show that the DNA is in the B form or modified B form. This was determined by Raman spectroscopy of chromatins, of nucleosomes (from calf thymus) and of DNA fibres and directly correlated with X-ray diffraction studies. The Raman spectra of three forms of DNA (A, B and C) have been characterized in fibres both by X-ray diffraction and Raman spectroscopy on the same sample. In particular, the Raman spectrum of the C form of DNA is characterized by a band of about 870 cm(-1). For the first time, chromatins of different origins with increasing content of non-histone proteins have been investigated by Raman spectroscopy. The site of interaction of the non-histone proteins appears to involve the N7 position of guanine while the histone core does not interact at this site. It is proposed that the mechanism of specific recognition in chromatin involves the large groove.     

Circular dichroism and DNA secondary structure.

The change in average rotation of the DNA helix has been determined for the transfer from 0.05 M NaCl to 3.0 M CsCl, 6.2 M LiCl and 5.4 M NH4Cl. This work, combined with data at lower salt from other laboratories, allows us to relate the intensity of the CD of DNA at 275 nm directly to the change in the number of base pairs per turn. The change in secondary structure for the transfer of DNA from 0.05 M NaCl (where it is presumably in the B-form) to high salt (where the characteristic CD has been interpreted as corresponding to C-form geometry) is found to be -0.22 (+/- 0.02) base pairs per turn. In the case of mononucleosomes, where the CD indicates the "C-form", the change in secondary structure (including temperature effects) would add -0.31 (+/- 0.03) turns about the histone core to the -1.25 turns estimated from work on SV40 chromatin. Accurate winding angles and molar extinction coefficients were determined for ethidium.     

The fractionation of calf thymus DNA by multiple formation of sedimentable complexes with homologous lysine-rich histone KAP. Derivative melting curves and ultracentrifugation in CsCl concentration gradients

The process of fractionation of total calf thymus DNA using a step precipitation of DNA by means of increasing concentrations of the homologous histone KAP was investigated. In addition to the known fractions three so far undescribed ones/in thymus/,characterized by buoyant densities in CsCl equal 1.692, 1.706 and 1.728 g/ccm, were identified. Considerable amounts of preparations seriously enriched in individual satellite fractions were obtained. The ability of GC-rich satellite DNAs to form more soluble complexes with histone KAP is suggested as reason for the observed fractionation.